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Commit e89c5e50 authored by Davide Lagoa's avatar Davide Lagoa
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Dockerfile
View file @ e89c5e50
FROM openjdk:10-slim
COPY ./code /home
WORKDIR /workdir
ADD ./requirements/system /workdir/system
ADD ./requirements/scraper /workdir/scraper
RUN apt-get -y update
RUN apt-get -y upgrade
RUN apt-get -y install ncbi-blast+
......
code/worker.py
View file @ e89c5e50
from flask import Flask
from flask import Flask, request, send_file, jsonify
import subprocess
import os
import shutil
import datetime
import logging
app = Flask(__name__)
PROCESS_PATH = '/home/transyt.py'
SUBMISSIONS_PATH = '/workdir/workerSubmissions/'
RESULTS_PATH = '/workdir/resultsWorker/'
#RESULTS_PATH = "C:\\Users\\BioSystems\\Desktop\\testFolder\\resultsWorker\\"
#SUBMISSIONS_PATH = "C:\\Users\\BioSystems\\Desktop\\testFolder\\workerSubmissions\\"
if not os.path.exists(SUBMISSIONS_PATH):
os.makedirs(SUBMISSIONS_PATH)
if not os.path.exists(RESULTS_PATH):
os.makedirs(RESULTS_PATH)
start_time = datetime.datetime.now()
running = False
@app.route("/start", methods=["POST"])
def start():
global start_time
global running
start_time = datetime.datetime.now()
if os.path.exists(SUBMISSIONS_PATH):
shutil.rmtree(SUBMISSIONS_PATH, ignore_errors=True)
if os.path.exists(RESULTS_PATH):
shutil.rmtree(RESULTS_PATH, ignore_errors=True)
os.makedirs(SUBMISSIONS_PATH)
os.makedirs(RESULTS_PATH)
@app.route("/start/<processingPath>/<resultsPath>")
def start(processingPath, resultsPath):
try:
resultsPath = resultsPath.replace('$', '/')
processingPath = processingPath.replace('$', '/')
subprocess.Popen(["python", PROCESS_PATH, processingPath, resultsPath])
for file in request.files.values():
destination = "/".join([SUBMISSIONS_PATH, file.filename])
file.save(destination)
subprocess.Popen(["python", PROCESS_PATH, SUBMISSIONS_PATH, RESULTS_PATH])
running = True
return ('processing', 102)
......@@ -20,5 +54,27 @@ def start(processingPath, resultsPath):
print('An error occurred while processing the submission')
return ('error', 500)
@app.route('/status')
def display_msg():
files = os.listdir(RESULTS_PATH)
if not running:
return jsonify({"result": "Not running"}), 410
if abs(datetime.datetime.now() - start_time) > datetime.timedelta(hours=2):
return jsonify({"result": "Time out"}), 408
if "processComplete" in files:
return send_file(RESULTS_PATH + "results.zip", as_attachment=True,
attachment_filename='results.zip'), 200
return jsonify({"result": "running"}), 202
@app.route('/handshake')
def handshake():
return jsonify({"result": "alive"}), 200
if __name__ == "__main__":
app.run(host="0.0.0.0", port=80, threaded=False, debug=True)
app.run(host="0.0.0.0", port=80, threaded=False, debug=True)
requirements/scraper/Family_Specific_Reactions/LastKnownVersion.log 0 → 100644
View file @ e89c5e50
familySpecificReactions_17h32m53s1922019.json
familySpecificReactions_16h38m48s2022019.json
familySpecificReactions_20h8m21s2522019.json
familySpecificReactions_23h22m59s2732019.json
familySpecificReactions_13h49m3s2832019.json
requirements/scraper/System_Specific_Reactions/LastKnownVersion.log 0 → 100644
View file @ e89c5e50
reactions_18h29m5s1922019.json
reactions_17h34m31s2022019.json
reactions_21h7m38s2522019.json
reactions_0h17m12s2832019.json
reactions_14h43m56s2832019.json
requirements/scraper/backup_files/TCDB_public_fasta/tcdbLastKnownVersion.log 0 → 100644
View file @ e89c5e50
tcdbFasta_10h42m19s1822019.faa
tcdbFasta_9h59m45s1922019.faa
tcdbFasta_9h53m32s2022019.faa
tcdbFasta_12h58m29s2522019.faa
tcdbFasta_13h2m47s2522019.faa
tcdbFasta_13h14m51s2522019.faa
tcdbFasta_15h14m33s2622019.faa
tcdbFasta_15h15m53s2622019.faa
tcdbFasta_16h40m58s2732019.faa
tcdbFasta_7h5m36s2832019.faa
requirements/scraper/backup_files/TCDB_systems_summary/LastKnownVersion.log 0 → 100644
View file @ e89c5e50
TCSystems_17h4m31s1922019.json
TCSystems_16h11m12s2022019.json
TCSystems_19h40m47s2522019.json
TCSystems_22h55m53s2732019.json
TCSystems_13h21m51s2832019.json
requirements/scraper/backup_files/TCFilesBackup/version__13h22m31s2832019/1.A.1.txt 0 → 100644
View file @ e89c5e50
This source diff could not be displayed because it is too large. You can view the blob instead.
requirements/scraper/backup_files/TCFilesBackup/version__13h22m31s2832019/1.A.100.txt 0 → 100644
View file @ e89c5e50
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html>
<head>
<title>TCDB &raquo; SEARCH</title>
<link type="text/css" rel="stylesheet" media="screen, projection" href="../css/tcdb.css">
<link type="text/css" rel="stylesheet" media="screen, projection" href="../css/tcdb-reset.css">
<script type="text/javascript" src="http://www.rcsb.org/pdb/widgets/rcsbPdbTagLib.js"></script>
<script type="text/javascript">
$(document).ready(function(){
$(".tcdb-header-nav .search").addClass("selected");
$(".toggle_container").hide();
$("div.trigger").toggle(function(){
$(this).addClass("active");
}, function () {
$(this).removeClass("active");
});
$("div.trigger").click(function(){
$(this).next(".toggle_container").slideToggle("slow,");
});
$("h4.trigger").toggle(function(){
$(this).addClass("active");
}, function () {
$(this).removeClass("active");
});
$("h4.trigger").click(function(){
$(this).next(".toggle_container").slideToggle("slow,");
});
});
</script>
</head>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-23543533-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
<div id="tcdb-header-wrap">
<div class="tcdb-header-search-wrap">
<div class="header-links">
<a href="/aboutus.php" title="Saier Lab. Bioinformatics Group">about</a> <span class="lsep">|</span> <a href="/faq.php" title="Frequently Asked Questions">faq</a>
</div>
<script type="text/javascript">
function formfocus() {
document.getElementById('query').focus();
}
window.onload = formfocus;
</script>
<div class="header-search">
<form id="search" name="search" action="/search/index.php" method="post">
<div>
<input name="query" id="query" class="textbox" tabindex="1" onfocus="if (this.value=='search') this.value = ''" type="text" value="search" title="Search with TC ID, UniProt #, PDB ID, etc." />
</div>
</form>
</div>
</div> <!-- tcdb-header-search-wrap -->
<a href="/"><div class="header-logo"></div></a>
<div class="tcdb-header-nav-wrap">
<div class="tcdb-header-nav">
<ul>
<li><a href="/" class="home" title="www.tcdb.org &raquo; home">Home</a></li>
<li><a href="/search/index.php" class="search" title="Search options">Search</a></li>
<li><a href="/superfamily.php" class="superfamilies" title="List of all TC-Superfamilies">Superfamilies</a></li>
<li><a href="/analyze.php" class="analyze" title="Analyze your sequence(s)">Analyze</a></li>
<li><a href="/browse.php" class="browse" title="Browse TC-System in tree mode">Browse</a></li>
</ul>
</div>
</div> <!-- tcdb-header-nav-wrap -->
<div style="clear:both;"></div>
<div id="saierlab-wrap">
<div class="saierlab">TCDB is operated by the <a href="/aboutus.php">Saier Lab Bioinformatics Group</a></div>
<div class="saierlab-line"></div>
</div>
</div> <!-- tcdb-header-wrap -->
<body>
<div id="main-wrap"> <!-- this is important! -->
<div id="tcdb-page-wrap">
<div id="search-result">
<div class="result">
<div class="print-format"><img src="../images/printer.png" width="16"><A HREF="/tcfamilybrowse.php?tc=1.A.100" target="_window" border="0">Format for Printing</A></div>
<div class="next-level"><a href="/search/result.php?tc=1.A.100.3">View Proteins belonging to: <span style="color:maroon;">The Rhabdoviridae Putative Viroporin, U5 (RV-U5) Family</span></a></div>
<!-- <div class="title">1.A.100: The Rhabdoviridae Putative Viroporin, U5 (RV-U5) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.100 The Rhabdoviridae Putative Viroporin, U5 (RV-U5) Family&nbsp;</strong></p>
<p>Viruses belonging to the family Rhabdoviridae infect a variety of
different hosts including insects, vertebrates and plants. There are over 200 rhabdoviruses isolated
around the world.&nbsp; The complete genome sequence
and predicted transcription strategy of Wongabel <span class='highlight'>virus</span> (WONV), a&nbsp; rhabdovirus isolated from biting
midges (<em>Culicoides austropalpalis</em>) is available. The 13,196 nucleotide genome encodes five typical
rhabdovirus genes N, P, M, G and L, plus three genes located between the P and M genes (U1, U2, U3) and
two overlapping the N and G genes (U4, U5). The U5 gene product has characteristics
typical of viroporins with structural similarities with the
alpha-1 <span class='highlight'>protein</span> (putative viroporin) of viruses in the genus Ephemerovirus, and similarity with the <span class='highlight'>avian</span>-associated Flanders <span class='highlight'>virus</span> has been noted (<a class="reflink" href="/search/result.php?tc=1.A.100#ref34544547">Gubala <em>et al.</em> 2008</a>).</p></div>
<div class="next-level-result">
</div>
<div class="next-level"><a href="/search/result.php?tc=1.A.100.3">View Proteins belonging to: <span style="color:maroon;">The Rhabdoviridae Putative Viroporin, U5 (RV-U5) Family</span></a></div>
<div class="tcdb-fam-ref">
<h4>References associated with 1.A.100 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34544547"></A>Gubala, A.J., D.F. Proll, R.T. Barnard, C.J. Cowled, S.G. Crameri, A.D. Hyatt, and D.B. Boyle. (2008). Genomic characterisation of Wongabel virus reveals novel genes within the Rhabdoviridae. Virology 376: 13-23. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=18436275" target="_window">18436275</A></div>
</div>
</div> <!-- tcdb-fam-ref -->
</div> <!-- result -->
</div> <!-- search-result -->
</div> <!-- tcdb-page-wrap -->
</div> <!-- main-wrap -->
<div id="tcdb-footer-wrap">
<div class="footer">
&copy; 2005 - 2019 Saier Lab.&nbsp;|&nbsp;<a href="/aboutus.php">Contact</a>&nbsp|&nbsp<a href="/faq.php">FAQ</a><br /><a href="/">TCDB.ORG</a> is maintained by Saier Lab. Group @ UCSD in collaboration with <a href="http://www.sdsc.edu/"><img src="/images/sdsc_logo.jpg"></a>
<br>The text of this website is available for modification and reuse under the terms of the Creative Commons Attribution-Sharealike 3.0 Unported License and the GNU Free Documentation License
</div>
</div>
</body>
</html>
requirements/scraper/backup_files/TCFilesBackup/version__13h22m31s2832019/1.A.101.txt 0 → 100644
View file @ e89c5e50
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html>
<head>
<title>TCDB &raquo; SEARCH</title>
<link type="text/css" rel="stylesheet" media="screen, projection" href="../css/tcdb.css">
<link type="text/css" rel="stylesheet" media="screen, projection" href="../css/tcdb-reset.css">
<script type="text/javascript" src="http://www.rcsb.org/pdb/widgets/rcsbPdbTagLib.js"></script>
<script type="text/javascript">
$(document).ready(function(){
$(".tcdb-header-nav .search").addClass("selected");
$(".toggle_container").hide();
$("div.trigger").toggle(function(){
$(this).addClass("active");
}, function () {
$(this).removeClass("active");
});
$("div.trigger").click(function(){
$(this).next(".toggle_container").slideToggle("slow,");
});
$("h4.trigger").toggle(function(){
$(this).addClass("active");
}, function () {
$(this).removeClass("active");
});
$("h4.trigger").click(function(){
$(this).next(".toggle_container").slideToggle("slow,");
});
});
</script>
</head>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-23543533-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
<div id="tcdb-header-wrap">
<div class="tcdb-header-search-wrap">
<div class="header-links">
<a href="/aboutus.php" title="Saier Lab. Bioinformatics Group">about</a> <span class="lsep">|</span> <a href="/faq.php" title="Frequently Asked Questions">faq</a>
</div>
<script type="text/javascript">
function formfocus() {
document.getElementById('query').focus();
}
window.onload = formfocus;
</script>
<div class="header-search">
<form id="search" name="search" action="/search/index.php" method="post">
<div>
<input name="query" id="query" class="textbox" tabindex="1" onfocus="if (this.value=='search') this.value = ''" type="text" value="search" title="Search with TC ID, UniProt #, PDB ID, etc." />
</div>
</form>
</div>
</div> <!-- tcdb-header-search-wrap -->
<a href="/"><div class="header-logo"></div></a>
<div class="tcdb-header-nav-wrap">
<div class="tcdb-header-nav">
<ul>
<li><a href="/" class="home" title="www.tcdb.org &raquo; home">Home</a></li>
<li><a href="/search/index.php" class="search" title="Search options">Search</a></li>
<li><a href="/superfamily.php" class="superfamilies" title="List of all TC-Superfamilies">Superfamilies</a></li>
<li><a href="/analyze.php" class="analyze" title="Analyze your sequence(s)">Analyze</a></li>
<li><a href="/browse.php" class="browse" title="Browse TC-System in tree mode">Browse</a></li>
</ul>
</div>
</div> <!-- tcdb-header-nav-wrap -->
<div style="clear:both;"></div>
<div id="saierlab-wrap">
<div class="saierlab">TCDB is operated by the <a href="/aboutus.php">Saier Lab Bioinformatics Group</a></div>
<div class="saierlab-line"></div>
</div>
</div> <!-- tcdb-header-wrap -->
<body>
<div id="main-wrap"> <!-- this is important! -->
<div id="tcdb-page-wrap">
<div id="search-result">
<div class="result">
<div class="print-format"><img src="../images/printer.png" width="16"><A HREF="/tcfamilybrowse.php?tc=1.A.101" target="_window" border="0">Format for Printing</A></div>
<div class="next-level"><a href="/search/result.php?tc=1.A.101.8">View Proteins belonging to: <span style="color:maroon;">The Peroxisomal Pore-forming Pex11 (Pex11) Family</span></a></div>
<!-- <div class="title">1.A.101: The Peroxisomal Pore-forming Pex11 (Pex11) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.101 The Peroxisomal Pore-forming Pex11 (Pex11) Family</strong></p>
<p>More than thirty Pex proteins are known to participate in the biogenesis of peroxisomes, oxidative organelles involved in lipid and ROS metabolism. Pex11 homologues are constituents of the Pexoxisomal Protein Importer (PPI) Family (TC# 3.A.20). They play roles, direct or indirect, in division and proliferation of peroxisomes (<a class="reflink" href="/search/result.php?tc=1.A.101#ref34544772">Schrader <em>et al.</em> 1998</a>).&nbsp;<a class="reflink" href="/search/result.php?tc=1.A.101#ref34544773">Mindthoff <em>et al.</em> 2015</a> showed that yeast Pex11 is a
pore-forming protein, possibly sharing significant sequence similarity with TRPM cation-selective channels. The Pex11
channel is moderately cation-selective
(PK<sup>+</sup>/PCl<sup>-</sup>=1.85) and resistant to voltage-dependent closing. The estimated size of the channel's pore
(r~0.6nm) supports the notion that Pex11 conducts solutes with molecular mass below 300-400 Da, and the channel's selectivity filter was localized. Overproduction of Pex11 resulted in acceleration of
fatty acids beta-oxidation in intact cells but not in the corresponding lysates. Beta-oxidation in cells was affected by expression of the Pex11 protein carrying point mutations in the selectivity
filter. These data suggested that the Pex11-dependent transmembrane traffic of metabolites may be a
rate-limiting step in the beta-oxidation of fatty acids. This conclusion was corroborated by
analysis of the rate of beta-oxidation in yeast strains expressing Pex11 with mutations mimicking
constitutively phosphorylated (S165D, S167D) or unphosphorylated (S165A, S167A) protein. The results
suggest that phosphorylation of Pex11 is a mechanism that can control the peroxisomal beta-oxidation
rate.&nbsp; Pex11 is thus a non-selective channel responsible
for transfer of metabolites across peroxisomal membrane.(<a class="reflink" href="/search/result.php?tc=1.A.101#ref34544773">Mindthoff <em>et al.</em> 2015</a>).</p></div>
<div class="result-superfam">This family belongs to the:<a href="/superfamily.php?id=76"> Peroxisomal Peroxin (Pex)11/25/27 (Pex11/25/27) Superfamily</a>.</div>
<div class="next-level-result">
</div>
<div class="next-level"><a href="/search/result.php?tc=1.A.101.8">View Proteins belonging to: <span style="color:maroon;">The Peroxisomal Pore-forming Pex11 (Pex11) Family</span></a></div>
<div class="tcdb-fam-ref">
<h4>References associated with 1.A.101 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34545748"></A>Jaiteh, M., A. Taly, and J. Hénin. (2016). Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors. PLoS One 11: e0151934. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26986966" target="_window">26986966</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34544773"></A>Mindthoff S., Grunau S., Steinfort LL., Girzalsky W., Hiltunen JK., Erdmann R. and Antonenkov VD. (2015). Peroxisomal Pex11 is a pore-forming protein homologous to TRPM channels. Biochim Biophys Acta. 1863(2):271-283. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26597702" target="_window">26597702</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34544772"></A>Schrader, M., B.E. Reuber, J.C. Morrell, G. Jimenez-Sanchez, C. Obie, T.A. Stroh, D. Valle, T.A. Schroer, and S.J. Gould. (1998). Expression of PEX11beta mediates peroxisome proliferation in the absence of extracellular stimuli. J. Biol. Chem. 273: 29607-29614. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=9792670" target="_window">9792670</A></div>
</div>
</div> <!-- tcdb-fam-ref -->
</div> <!-- result -->
</div> <!-- search-result -->
</div> <!-- tcdb-page-wrap -->
</div> <!-- main-wrap -->
<div id="tcdb-footer-wrap">
<div class="footer">
&copy; 2005 - 2019 Saier Lab.&nbsp;|&nbsp;<a href="/aboutus.php">Contact</a>&nbsp|&nbsp<a href="/faq.php">FAQ</a><br /><a href="/">TCDB.ORG</a> is maintained by Saier Lab. Group @ UCSD in collaboration with <a href="http://www.sdsc.edu/"><img src="/images/sdsc_logo.jpg"></a>
<br>The text of this website is available for modification and reuse under the terms of the Creative Commons Attribution-Sharealike 3.0 Unported License and the GNU Free Documentation License
</div>
</div>
</body>
</html>
requirements/scraper/backup_files/TCFilesBackup/version__13h22m31s2832019/1.A.102.txt 0 → 100644
View file @ e89c5e50
<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html>
<head>
<title>TCDB &raquo; SEARCH</title>
<link type="text/css" rel="stylesheet" media="screen, projection" href="../css/tcdb.css">
<link type="text/css" rel="stylesheet" media="screen, projection" href="../css/tcdb-reset.css">
<script type="text/javascript" src="http://www.rcsb.org/pdb/widgets/rcsbPdbTagLib.js"></script>
<script type="text/javascript">
$(document).ready(function(){
$(".tcdb-header-nav .search").addClass("selected");
$(".toggle_container").hide();
$("div.trigger").toggle(function(){
$(this).addClass("active");
}, function () {
$(this).removeClass("active");
});
$("div.trigger").click(function(){
$(this).next(".toggle_container").slideToggle("slow,");
});
$("h4.trigger").toggle(function(){
$(this).addClass("active");
}, function () {
$(this).removeClass("active");
});
$("h4.trigger").click(function(){
$(this).next(".toggle_container").slideToggle("slow,");
});
});
</script>
</head>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push(['_setAccount', 'UA-23543533-1']);
_gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script>
<div id="tcdb-header-wrap">
<div class="tcdb-header-search-wrap">
<div class="header-links">
<a href="/aboutus.php" title="Saier Lab. Bioinformatics Group">about</a> <span class="lsep">|</span> <a href="/faq.php" title="Frequently Asked Questions">faq</a>
</div>
<script type="text/javascript">
function formfocus() {
document.getElementById('query').focus();
}
window.onload = formfocus;
</script>
<div class="header-search">
<form id="search" name="search" action="/search/index.php" method="post">
<div>
<input name="query" id="query" class="textbox" tabindex="1" onfocus="if (this.value=='search') this.value = ''" type="text" value="search" title="Search with TC ID, UniProt #, PDB ID, etc." />
</div>
</form>
</div>
</div> <!-- tcdb-header-search-wrap -->
<a href="/"><div class="header-logo"></div></a>
<div class="tcdb-header-nav-wrap">
<div class="tcdb-header-nav">
<ul>
<li><a href="/" class="home" title="www.tcdb.org &raquo; home">Home</a></li>
<li><a href="/search/index.php" class="search" title="Search options">Search</a></li>
<li><a href="/superfamily.php" class="superfamilies" title="List of all TC-Superfamilies">Superfamilies</a></li>
<li><a href="/analyze.php" class="analyze" title="Analyze your sequence(s)">Analyze</a></li>
<li><a href="/browse.php" class="browse" title="Browse TC-System in tree mode">Browse</a></li>
</ul>
</div>
</div> <!-- tcdb-header-nav-wrap -->
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<div class="next-level"><a href="/search/result.php?tc=1.A.102.1">View Proteins belonging to: <span style="color:maroon;">The Influenza A viroporin PB1-F2 (PB1-F2) Family</span></a></div>
<!-- <div class="title">1.A.102: The Influenza A viroporin PB1-F2 (PB1-F2) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.102 The Influenza A viroporin PB1-F2 (PB1-F2) Family</strong></p>
<p>The PB1-F2 protein of 90 aas, and possibly a weakly hydrophobic C-terminal TMS, exhibits viroporin activity, transporting monovalent cations and Ca<sup>2+ </sup>(<a class="reflink" href="/search/result.php?tc=1.A.102#ref34545079">Hyser and Estes 2015</a>).&nbsp;</p></div>
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<div class="tcdb-fam-ref">
<h4>References associated with 1.A.102 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34545080"></A>Hyser, J.M. and M.K. Estes. (2015). Pathophysiological Consequences of Calcium-Conducting Viroporins. Annu Rev Virol 2: 473-496. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26958925" target="_window">26958925</A></div>
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requirements/scraper/backup_files/TCFilesBackup/version__13h22m31s2832019/1.A.103.txt 0 → 100644
View file @ e89c5e50
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<div class="next-level"><a href="/search/result.php?tc=1.A.103.1">View Proteins belonging to: <span style="color:maroon;">The Simian Virus 5 (Parainfluenza Virus 5) SH (SV5-SH) Family</span></a></div>
<!-- <div class="title">1.A.103: The Simian Virus 5 (Parainfluenza Virus 5) SH (SV5-SH) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.103 The Simian Virus 5 (Parainfluenza Virus 5) SH (SV5-SH) Family</strong>&nbsp;</p>
<p>The SV5-SH family consists of short (44 aa) proteins with one C-terminal TMS that form viroporins that transport monovalent cations (<a class="reflink" href="/search/result.php?tc=1.A.103#ref34545079">Hyser and Estes 2015</a>).</p></div>
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<div class="tcdb-fam-ref">
<h4>References associated with 1.A.103 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34545085"></A>Hyser, J.M. and M.K. Estes. (2015). Pathophysiological Consequences of Calcium-Conducting Viroporins. Annu Rev Virol 2: 473-496. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26958925" target="_window">26958925</A></div>
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requirements/scraper/backup_files/TCFilesBackup/version__13h22m31s2832019/1.A.104.txt 0 → 100644
View file @ e89c5e50
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<div class="next-level"><a href="/search/result.php?tc=1.A.104.1">View Proteins belonging to: <span style="color:maroon;">The Proposed Flagellar Biosynthesis Na+ Channel, FlaH (FlaH) Family</span></a></div>
<!-- <div class="title">1.A.104: The Proposed Flagellar Biosynthesis Na+ Channel, FlaH (FlaH) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.104 The Proposed Flagellar Biosynthesis Na<sup>+</sup> Channel, FlhA (FlhA) Family&nbsp;</strong></p>
<p>The flagellar type III export apparatus utilizes ATP and the proton motive force (PMF) to
transport flagellar proteins to the distal end of the growing flagellar structure for self-assembly.
The transmembrane export gate complex is a H<sup>+</sup>-protein antiporter. Activity is greatly
augmented by an associated cytoplasmic ATPase complex.&nbsp;<a class='reflink' href='../../search/#ref34545097'>Minamino <em>et al.</em> 2016</a> reported that the export gate complex
can use the sodium motive force (SMF) in addition to the PMF to drive
protein export. Protein export was considerably reduced in the absence of the ATPase complex and a
pH gradient across the membrane, but Na<sup>+</sup> increased it dramatically. Phenamil, a blocker of Na<sup>+</sup> translocation, inhibited protein export. Overexpression of FlhA increased the intracellular Na<sup>+</sup> concentration in the presence of 100 mM external NaCl but not in its absence, suggesting that FlhA acts as a
Na<sup>+</sup> channel. In wild-type cells, however, neither Na<sup>+</sup> nor phenamil affected protein export,
indicating that the Na<sup>+</sup> channel activity of FlhA is suppressed by the ATPase complex. <a class='reflink' href='../../search/#ref34545097'>Minamino <em>et al.</em> 2016</a> proposed
that the export gate by itself is a dual fuel engine that uses both the PMF and the SMF for protein export,
and that the ATPase complex switches this dual fuel engine into a PMF-driven export machinery to
become much more robust against environmental changes in external pH and Na<sup>+</sup> concentration.</p></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.104.1">View Proteins belonging to: <span style="color:maroon;">The Proposed Flagellar Biosynthesis Na+ Channel, FlaH (FlaH) Family</span></a></div>
<div class="tcdb-fam-ref">
<h4>References associated with 1.A.104 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34545098"></A>Minamino, T., Y.V. Morimoto, N. Hara, P.D. Aldridge, and K. Namba. (2016). The Bacterial Flagellar Type III Export Gate Complex Is a Dual Fuel Engine That Can Use Both H<sup>+</sup> and Na<sup>+</sup> for Flagellar Protein Export. PLoS Pathog 12: e1005495. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26943926" target="_window">26943926</A></div>
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<br>The text of this website is available for modification and reuse under the terms of the Creative Commons Attribution-Sharealike 3.0 Unported License and the GNU Free Documentation License
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requirements/scraper/backup_files/TCFilesBackup/version__13h22m31s2832019/1.A.105.txt 0 → 100644
View file @ e89c5e50
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<div class="next-level"><a href="/search/result.php?tc=1.A.105.1">View Proteins belonging to: <span style="color:maroon;">The Mixed Lineage Kinase Domain-like (MLKL) Family</span></a></div>
<!-- <div class="title">1.A.105: The Mixed Lineage Kinase Domain-like (MLKL) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.105 The Mixed Lineage Kinase Domain-like (MLKL) Family&nbsp;</strong></p>
<p>The mixed lineage kinase domain-like (MLKL) protein is a key factor in tumor necrosis factor-induced
necroptosis. Studies on necroptosis execution revealed a commitment role of MLKL in membrane
disruption. <a class="reflink" href="/search/result.php?tc=1.A.105#ref34545310">Xia <em>et al.</em> 2016</a> demonstrated that MLKL forms cation channels that are permeable preferentially to Mg<sup>2+</sup> rather than
Ca<sup>2+</sup> in the presence of Na<sup>+</sup> and K<sup>+</sup>. Moreover, the N-terminal domain containing six helices (H1-H6)
is sufficient to form channels. Using the substituted cysteine accessibility method, helix H1, H2, H3, H5 and H6 appeared to be transmembrane segments, while H4 is located in the
cytoplasm. Finally, MLKL-induced membrane depolarization and cell death exhibit a positive
correlation to its channel activity. The Mg<sup>2+</sup>-preferred permeability and five transmembrane segment
topology distinguish MLKL from previously identified Mg<sup>2+</sup>-permeable channels and thus establish MLKL
as a novel class of cation channels.</p></div>
<div class="result-superfam">This family belongs to the:<a href="/superfamily.php?id=92"> Ankyrin Repeat Domain-containing (Ank) Family, found in at least some proteins in the following TC families </a>.</div>
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</div>
<div class="next-level"><a href="/search/result.php?tc=1.A.105.1">View Proteins belonging to: <span style="color:maroon;">The Mixed Lineage Kinase Domain-like (MLKL) Family</span></a></div>
<div class="tcdb-fam-ref">
<h4>References associated with 1.A.105 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34545310"></A>Xia, B., S. Fang, X. Chen, H. Hu, P. Chen, H. Wang, and Z. Gao. (2016). MLKL forms cation channels. Cell Res 26: 517-528. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=27033670" target="_window">27033670</A></div>
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requirements/scraper/backup_files/TCFilesBackup/version__13h22m31s2832019/1.A.106.txt 0 → 100644
View file @ e89c5e50
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<div class="next-level"><a href="/search/result.php?tc=1.A.106.2">View Proteins belonging to: <span style="color:maroon;">The Calcium Load-activated Calcium Channel (CLAC) Family </span></a></div>
<!-- <div class="title">1.A.106: The Calcium Load-activated Calcium Channel (CLAC) Family </div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.106 The Calcium Load-activated Calcium Channel (CLAC) Family&nbsp;</strong></p>
<p>Maintaining homeostasis of Ca<sup>2+</sup> stores in the endoplasmic reticulum (ER) is crucial for proper
Ca<sup>2+</sup> signaling and key cellular functions. The Ca<sup>2+</sup>-release-activated Ca<sup>2+</sup> (CRAC) channel is
responsible for Ca<sup>2+</sup> influx and refilling after store depletion. Transmembrane and coiled-coil domains protein 1 (TMCO1) is an ER transmembrane protein with 3 TMSs
that actively prevents Ca<sup>2+</sup> stores from overfilling, acting as a 'Cacium Load-activated Calcium channel' or 'CLAC' channel. TMCO1 undergoes reversible homotetramerization in
response to ER Ca<sup>2+</sup> overloading and disassembly upon Ca<sup>2+</sup> depletion and forms a Ca<sup>2+</sup>-selective
ion channel in liposomes. TMCO1 knockout mice reproduce the main clinical features of human
cerebrofaciothoracic (CFT) dysplasia spectrum, a developmental disorder linked to TMCO1 dysfunction,
and exhibit severe mishandling of ER Ca<sup>2+</sup> in cells. Thus, TMCO1 provides a
protective mechanism to prevent overfilling of ER stores with Calcium ions (<a class="reflink" href="/search/result.php?tc=1.A.106#ref34545417">Wang <em>et al.</em> 2016</a>).&nbsp; The CLAC Family was formerly the DUF106 Family.</p></div>
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<div class="tcdb-fam-ref">
<h4>References associated with 1.A.106 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34547896"></A>Sun, Z., H. Zhang, X. Wang, Q.C. Wang, C. Zhang, J.Q. Wang, Y.H. Wang, C.Q. An, K.Y. Yang, Y. Wang, F. Gao, C. Guo, and T.S. Tang. (2018). TMCO1 is essential for ovarian follicle development by regulating ER Castore of granulosa cells. Cell Death Differ. [Epub: Ahead of Print] <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=29467381" target="_window">29467381</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34545417"></A>Wang, Q.C., Q. Zheng, H. Tan, B. Zhang, X. Li, Y. Yang, J. Yu, Y. Liu, H. Chai, X. Wang, Z. Sun, J.Q. Wang, S. Zhu, F. Wang, M. Yang, C. Guo, H. Wang, Q. Zheng, Y. Li, Q. Chen, A. Zhou, and T.S. Tang. (2016). TMCO1 Is an ER Ca<sup>2+</sup> Load-Activated Ca<sup>2+</sup> Channel. Cell 165: 1454-1466. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=27212239" target="_window">27212239</A></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.107.1">View Proteins belonging to: <span style="color:maroon;">The Pore-forming Globin (Globin) Family</span></a></div>
<!-- <div class="title">1.A.107: The Pore-forming Globin (Globin) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.107 The Pore-forming Globin (Globin) Family&nbsp;</strong></p>
<p>Globins contain one or more cavities that control or affect such functions as ligand movement and
ligand binding. <a class="reflink" href="/search/result.php?tc=1.A.107#ref34545822">Morrill and Kostellow 2016</a> reported that the extended globin family [cytoglobin (Cygb); neuroglobin
(Ngb); myoglobin (Mb); hemoglobin (Hb) subunits Hba(alpha); and Hbb(beta)] contain either a
transmembrane (TM) helix or pore-lining region as well as internal cavities. Protein motif/domain
analyses indicate that Ngb and Hbb each contain 5 cholesterol-binding (CRAC/CARC) domains and 1
caveolin binding motif, whereas the Cygb dimer has 6 cholesterol-binding domains but lacks caveolin-
binding motifs. Mb and Hba each exhibit 2 cholesterol-binding domains and also lack caveolin-binding
motifs. The Hb &alpha;&beta;-tetramer contains 14 cholesterol-binding domains. Computer algorithms
indicate that Cygb and Ngb cavities display multiple partitions and C-terminal pore-lining regions,
whereas Mb has three major cavities plus a C-terminal pore-lining region. The Hb tetramer exhibits a
large internal cavity but the subunits differ in that they contain a C-terminal TM helix (Hba) and
pore-lining region (Hbb). The cavities include 43 of 190 Cygb residues, 38 of 151 of Ngb residues,
55 of 154 Mb residues, and 137 of 688 residues in the Hb tetramer. Each cavity complex includes 6 to
8 residues of the TM helix or pore-lining region and CRAC/CARC domains exist within all cavities.
Erythrocyte Hb &alpha;&beta;-tetramers are largely cytosolic but also bind to a membrane anion exchange
protein, 'band 3,' which contains a large internal cavity and 12 TM helices (5 being pore-lining
regions). The Hba TM helix may be the erythrocyte membrane 'band 3' attachment site. 'Band 3'
contributes 4 caveolin binding motifs and 10 CRAC/CARC domains. Cholesterol binding may create
lipid-disordered phases that alter globin cavities and facilitate ligand movement, permitting ion
channel formation and conformational changes that orchestrate anion and ligand (O2, CO2, NO)
movement within the large internal cavities and channels of the globins (<a class="reflink" href="/search/result.php?tc=1.A.107#ref34545822">Morrill and Kostellow 2016</a>).</p></div>
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<div class="tcdb-fam-ref">
<h4>References associated with 1.A.107 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34545822"></A>Morrill, G.A. and A.B. Kostellow. (2016). Molecular Properties of Globin Channels and Pores: Role of Cholesterol in Ligand Binding and Movement. Front Physiol 7: 360. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=27656147" target="_window">27656147</A></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.108.1">View Proteins belonging to: <span style="color:maroon;">The Fibroblast Growth Factor 2 (FGF2) Family</span></a></div>
<!-- <div class="title">1.A.108: The Fibroblast Growth Factor 2 (FGF2) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.108.&nbsp; The Fibroblast Growth Factor 2 (FGF2) Family</strong></p>
<p>Unconventional secretory proteins lack signal peptides and their export
from cells is not affected by brefeldin A, an inhibitor of protein
transport along the classical secretory pathway (<a class="reflink" href="/search/result.php?tc=1.A.108#ref34546949">Nickel 2010</a>). Export can be mediated by direct
translocation across plasma membranes of cytoplasmic proteins such as <span class='highlight'>fibroblast growth factor 2</span> which can be modified by phosphorylation involving the Tec protein kinase (<a class="reflink" href="/search/result.php?tc=1.A.108#ref34546955">La Venuta <em>et al.</em> 2016</a>) so that it inserts into membranes, creating oligomeric pores that are intermediates in the secretion process (see&nbsp;<a class="reflink" href="/search/result.php?tc=1.A.108#ref34546951">Nickel and Seedorf 2008</a> and TC# 9.A.48). Tyrosyl phosphorylation of FGF2 followed by association with phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) triggers formation of a lipidic membrane pore, essential for FGF2 secretion (<a class="reflink" href="/search/result.php?tc=1.A.108#ref34546950">Steringer <em>et al.</em> 2012</a>). Formation of disulfide bridges is also essential for this process (<a class="reflink" href="/search/result.php?tc=1.A.108#ref34546952">M&uuml;ller <em>et al.</em> 2015</a>). The cytoplasmic domain of the Na+/K+ ATPase, ATP1A1 (&alpha;-subunit) may function as a direct interaction receptor for the process (<a class="reflink" href="/search/result.php?tc=1.A.108#ref34546953">Zacherl <em>et al.</em> 2015</a>). Extracellular FGF2 is trapped by cell surface proteoglycans, and it then plays a role in tumor-indiced angiogenesis (<a class="reflink" href="/search/result.php?tc=1.A.108#ref34546954">La Venuta <em>et al.</em> 2015</a>). Proteoglycans may also play a role in the secretion of the cytoskeletal Alzheimer's disease-associated tau protein (P10636; <a class="reflink" href="/search/result.php?tc=1.A.108#ref34546960">Pompa <em>et al.</em> 2017</a>). Tau secretion correlated with tau phosphorylation and aggregation (<a class="reflink" href="/search/result.php?tc=1.A.108#ref34546962">Hannan <em>et al.</em> 2016</a>).</p>
<p>Alpha-Klotho (&alpha;-Klotho) is a member of the Klotho family consisting of this protein and two other single-pass transmembrane proteins: betaKlotho (&beta;-Klotho) and gammaKlotho (&gamma;-Klotho); &alpha;-Klotho circulates in the blood. FGF23 is a member of the FGF superfamily of 22 genes/proteins. &alpha;-Klotho serves as a co-receptor with FGF receptors (FGFRs) to provide a receptacle for physiological FGF23 signaling, including regulation of phosphate metabolism (<a class="reflink" href="/search/result.php?tc=1.A.108#ref34549093">Hu <em>et al.</em> 2018</a>). The extracellular domain of transmembrane &alpha;-Klotho is shed by secretases and released into blood circulation (soluble &alpha;-Klotho). Soluble alphaKlotho has both FGF23-independent and FGF23-dependent roles in phosphate homeostasis by modulating intestinal phosphate absorption, urinary phosphate excretion, and phosphate distribution into bone in concerted interactions with other calciophosphotropic hormones such as PTH and 1,25-(OH)2D. The direct role of alphaKlotho and FGF23 in the maintenance of phosphate homeostasis is partly mediated by modulation of type II Na<sup>+</sup>-dependent phosphate co-transporters in target organs. alphaKlotho and FGF23 are principal phosphotropic hormones, and manipulation of the alphaKlotho-FGF23 axis provides a therapeutic strategy for genetic and acquired phosphate disorders and for conditions with FGF23 excess or alphaKlotho deficiency such as chronic kidney disease (<a class="reflink" href="/search/result.php?tc=1.A.108#ref34549184">Hu <em>et al.</em> 2018</a>).</p></div>
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<div class="tcdb-fam-ref">
<h4>References associated with 1.A.108 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34546962"></A>Hannan, S.B., N.M. Dräger, T.M. Rasse, A. Voigt, and T.R. Jahn. (2016). Cellular and molecular modifier pathways in tauopathies: the big picture from screening invertebrate models. J Neurochem 137: 12-25. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26756400" target="_window">26756400</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34549184"></A>Hu, M.C., M. Shi, and O.W. Moe. (2018). Role of αKlotho and FGF23 in regulation of type II Na-dependent phosphate co-transporters. Pflugers Arch. [Epub: Ahead of Print] <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=30506274" target="_window">30506274</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546954"></A>La Venuta, G., M. Zeitler, J.P. Steringer, H.M. Müller, and W. Nickel. (2015). The Startling Properties of Fibroblast Growth Factor 2: How to Exit Mammalian Cells without a Signal Peptide at Hand. J. Biol. Chem. 290: 27015-27020. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26416892" target="_window">26416892</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546955"></A>La Venuta, G., S. Wegehingel, P. Sehr, H.M. Müller, E. Dimou, J.P. Steringer, M. Grotwinkel, N. Hentze, M.P. Mayer, D.W. Will, U. Uhrig, J.D. Lewis, and W. Nickel. (2016). Small Molecule Inhibitors Targeting Tec Kinase Block Unconventional Secretion of Fibroblast Growth Factor 2. J. Biol. Chem. 291: 17787-17803. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=27382052" target="_window">27382052</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546952"></A>Müller, H.M., J.P. Steringer, S. Wegehingel, S. Bleicken, M. Münster, E. Dimou, S. Unger, G. Weidmann, H. Andreas, A.J. García-Sáez, K. Wild, I. Sinning, and W. Nickel. (2015). Formation of disulfide bridges drives oligomerization, membrane pore formation, and translocation of fibroblast growth factor 2 to cell surfaces. J. Biol. Chem. 290: 8925-8937. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=25694424" target="_window">25694424</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546949"></A>Nickel, W. (2010). Pathways of unconventional protein secretion. Curr Opin Biotechnol 21: 621-626. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=20637599" target="_window">20637599</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546951"></A>Nickel, W. and M. Seedorf. (2008). Unconventional mechanisms of protein transport to the cell surface of eukaryotic cells. Annu. Rev. Cell Dev. Biol. 24: 287-308. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=18590485" target="_window">18590485</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546961"></A>Pompa, A., F. De Marchis, M.T. Pallotta, Y. Benitez-Alfonso, A. Jones, K. Schipper, K. Moreau, V. Žárský, G.P. Di Sansebastiano, and M. Bellucci. (2017). Unconventional Transport Routes of Soluble and Membrane Proteins and Their Role in Developmental Biology. Int J Mol Sci 18:. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=28346345" target="_window">28346345</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34547513"></A>Smith, E.R., S.G. Holt, and T.D. Hewitson. (2017). FGF23 activates injury-primed renal fibroblasts via FGFR4-dependent signalling and enhancement of TGF-β autoinduction. Int J Biochem. Cell Biol. 92: 63-78. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=28919046" target="_window">28919046</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546950"></A>Steringer, J.P., S. Bleicken, H. Andreas, S. Zacherl, M. Laussmann, K. Temmerman, F.X. Contreras, T.A. Bharat, J. Lechner, H.M. Müller, J.A. Briggs, A.J. García-Sáez, and W. Nickel. (2012). Phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2)-dependent oligomerization of fibroblast growth factor 2 (FGF2) triggers the formation of a lipidic membrane pore implicated in unconventional secretion. J. Biol. Chem. 287: 27659-27669. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=22730382" target="_window">22730382</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546953"></A>Zacherl, S., G. La Venuta, H.M. Müller, S. Wegehingel, E. Dimou, P. Sehr, J.D. Lewis, H. Erfle, R. Pepperkok, and W. Nickel. (2015). A direct role for ATP1A1 in unconventional secretion of fibroblast growth factor 2. J. Biol. Chem. 290: 3654-3665. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=25533462" target="_window">25533462</A></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.109.1">View Proteins belonging to: <span style="color:maroon;">The Interleukin 1 (IL1) Family</span></a></div>
<!-- <div class="title">1.A.109: The Interleukin 1 (IL1) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.109.&nbsp; The Interleukin 1 (IL1) Family&nbsp; </strong></p>
<p>Interleukin 1&alpha;, IL1A or IL1&alpha;, is p<span>roduced by activated macrophages, and IL-1 isoforms
stimulate thymocyte proliferation by inducing IL-2 release.
IL-1 proteins are involved in the inflammatory response, being
identified as endogenous pyrogens, and are reported to stimulate the
release of prostaglandin and collagenase from synovial cells.&nbsp; They also </span>disrupt the sertoli cell barrier/blood-testis
barrier by blocking Cx43 (TC# 1.A.24.1.1)-dependent gap junction communication (<a class="reflink" href="/search/result.php?tc=1.A.109#ref34546299">Chojnacka <em>et al.</em> 2016</a>)</p>
<p>Extracellular Interleukin-1&beta; (IL-1&beta;, IL1B, IL1F2), which regulates of the inflammatory
response, is secreted depending on the processing of a
precursor form following the activation of the multimolecular
inflammasome complex (see TC# 9.A.48). The secretion of IL-1&beta; after inflammasome activation requires
membrane permeabilization and occurs in parallel with the death of the
secreting cell. In macrophages, the release of IL-1&beta; in response to
inflammasome activation appears to be a secretory process independent
of nonspecific leakage of proteins during cell death. The mechanism of
membrane permeabilization leading to IL-1&beta; release is distinct from the
unconventional secretory mechanism employed by its structural homologues
fibroblast growth factor 2 (FGF2) or IL-1&alpha;, a process that involves the
formation of membrane pores but does not result in cell death (<a class="reflink" href="/search/result.php?tc=1.A.109#ref34546957">Mart&iacute;n-S&aacute;nchez <em>et al.</em> 2016</a>).</p></div>
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<div class="tcdb-fam-ref">
<h4>References associated with 1.A.109 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34546958"></A>Chojnacka, K., B. Bilinska, and D.D. Mruk. (2016). Interleukin 1α-induced disruption of the Sertoli cell cytoskeleton affects gap junctional communication. Cell Signal 28: 469-480. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26879129" target="_window">26879129</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546959"></A>Martín-Sánchez, F., C. Diamond, M. Zeitler, A.I. Gomez, A. Baroja-Mazo, J. Bagnall, D. Spiller, M. White, M.J. Daniels, A. Mortellaro, M. Peñalver, P. Paszek, J.P. Steringer, W. Nickel, D. Brough, and P. Pelegrín. (2016). Inflammasome-dependent IL-1β release depends upon membrane permeabilisation. Cell Death Differ 23: 1219-1231. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26868913" target="_window">26868913</A></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.110.1">View Proteins belonging to: <span style="color:maroon;">The Channel-forming Otopetrin (OTOP) Family</span></a></div>
<!-- <div class="title">1.A.110: The Channel-forming Otopetrin (OTOP) Family</div> -->
<div class="description"><p style="text-align: center;"><strong>1.A.110.&nbsp; The Channel-forming Otopetrin (OTOP) Family&nbsp; </strong></p>
<p>Otopertrin1 of <em>Danio rerio </em><span>inhibits P2Y purinoceptors. It has been reprted to modulate calcium homeostasis and influx of calcium in response to extracellular
ATP. It is essential for the formation of otoliths in the
inner ear of developing larvae and for the perception of gravity and
acceleration (<a class="reflink" href="/search/result.php?tc=1.A.110#ref34547901">S&ouml;llner <em>et al.</em> 2004</a>; ).&nbsp; </span><span>Otoliths in bony fishes and otoconia in mammals are composite crystals
consisting of calcium carbonate and proteins. These biominerals are part
of the gravity and linear acceleration detection system of the inner
ear. Mutations in otopetrin 1 result in lack of
otoconia in tilted and mergulhador mutant mice. </span><span><span><a class="reflink" href="/search/result.php?tc=1.A.110#ref34547901">S&ouml;llner <em>et al.</em> 2004</a></span> showed that a
mutation in the orthologous gene in zebrafish is responsible for the
complete absence of otoliths. They </span><span>examined the
localization of Starmaker, a secreted protein that is abundant in
otoliths in backstroke mutants. The starmaker protein accumulated within
cells of the otic epithelium, indicating a possible defect in secretion. </span></p>
<p>The fish inner ear contains three large extracellular biomineral
particles, otoliths, which have evolved to transduce the force of
gravity into neuronal signals. Mammalian ears contain thousands of small
particles called otoconia that serve a similar function. Loss or
displacement of these structures can be lethal for fish and is
responsible for benign paroxysmal positional vertigo (BPPV) in humans.
The distinct morphologies of otoconial particles and otoliths suggest
divergent developmental mechanisms. Mutations in Otopetrin 1 result in
nonsyndromic otoconial agenesis and a severe balance disorder in mice.&nbsp;<a class="reflink" href="/search/result.php?tc=1.A.110#ref34547902">Hughes <em>et al.</em> 2004</a> showed that in zebrafish,&nbsp; Otop1 is essential for otolith formation.
Morpholino-mediated knockdown of zebrafish Otop1 led to otolith
agenesis without affecting the sensory epithelium or other structures
within the inner ear. Otop1 regulates cellular Ca<sup>2+</sup> (<a class="reflink" href="/search/result.php?tc=1.A.110#ref34547903">Hughes <em>et al.</em> 2007</a>). The OTOP family was previously the DUF270 or pfam03189 family. The members of this family have three "<span class="highlight">Otopetrin</span> Domains" that are highly conserved between vertebrates, arthropods and
nematodes, as well as a constrained predicted loop structure (<a class="reflink" href="/search/result.php?tc=1.A.110#ref34547904">Hughes <em>et al.</em> 2008</a>).&nbsp;</p>
<p>By comparative transcriptome analysis of mouse taste receptor cells,&nbsp;<a class="reflink" href="/search/result.php?tc=1.A.110#ref34547905">Tu <em>et al.</em> 2018</a> identified OTOP1 as a
proton-selective ion channel. They found that murine OTOP1 is enriched in
acid-detecting taste receptor cells and is required for their
zinc-sensitive proton conductance. Two related murine genes, <em>Otop2</em> and <em>Otop3</em>, and a <em>Drosophila</em> ortholog also encode proton channels. Evolutionary conservation of the
gene family and its widespread tissue distribution suggest a broad role
for proton channels in physiology and pathophysiology (<a class="reflink" href="/search/result.php?tc=1.A.110#ref34547905">Tu <em>et al.</em> 2018</a>).</p></div>
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<div class="tcdb-fam-ref">
<h4>References associated with 1.A.110 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34547902"></A>Hughes, I., B. Blasiole, D. Huss, M.E. Warchol, N.P. Rath, B. Hurle, E. Ignatova, J.D. Dickman, R. Thalmann, R. Levenson, and D.M. Ornitz. (2004). Otopetrin 1 is required for otolith formation in the zebrafish <i>Danio rerio</i>. Dev Biol 276: 391-402. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=15581873" target="_window">15581873</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34547904"></A>Hughes, I., J. Binkley, B. Hurle, E.D. Green, , A. Sidow, and D.M. Ornitz. (2008). Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members. BMC Evol Biol 8: 41. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=18254951" target="_window">18254951</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34547903"></A>Hughes, I., M. Saito, P.H. Schlesinger, and D.M. Ornitz. (2007). Otopetrin 1 activation by purinergic nucleotides regulates intracellular calcium. Proc. Natl. Acad. Sci. USA 104: 12023-12028. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=17606897" target="_window">17606897</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34547901"></A>Söllner, C., H. Schwarz, R. Geisler, and T. Nicolson. (2004). Mutated otopetrin 1 affects the genesis of otoliths and the localization of Starmaker in zebrafish. Dev Genes Evol 214: 582-590. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=15480759" target="_window">15480759</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34547905"></A>Tu, Y.H., A.J. Cooper, B. Teng, R.B. Chang, D.J. Artiga, H.N. Turner, E.M. Mulhall, W. Ye, A.D. Smith, and E.R. Liman. (2018). An evolutionarily conserved gene family encodes proton-selective ion channels. Science 359: 1047-1050. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=29371428" target="_window">29371428</A></div>
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<br>The text of this website is available for modification and reuse under the terms of the Creative Commons Attribution-Sharealike 3.0 Unported License and the GNU Free Documentation License
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<div class="next-level"><a href="/search/result.php?tc=1.A.111.1">View Proteins belonging to: <span style="color:maroon;">The Reactive Oxygen Species Modulator 1 (Romo1) Family </span></a></div>
<!-- <div class="title">1.A.111: The Reactive Oxygen Species Modulator 1 (Romo1) Family </div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.111.&nbsp;</strong> <strong>The Reactive Oxygen Species Modulator 1 (Romo1) Family </strong></p>
<p><a class="reflink" href="/search/result.php?tc=1.A.111#ref11371">Zhao <em>et al.</em> 2009</a> identified a
human nuclear gene (named MTGM or ROMO1) that encodes a small (79 aa) integral 2 TMS mitochondrial inner-membrane
protein that shows high expression in both human brain tumor cell lines and tumor tissues. The gene
is evolutionarily highly conserved, and its orthologs are 100% identical at the amino acid level in
all analyzed mammalian species. The gene product is characterized by an unusual tetrad of the GxxxG
motif in the transmembrane segment. Overexpression of the MTGM (mitochondrial targeting GxxxG motif)
protein results in mitochondrial fragmentation and release of mitochondrial Smac/Diablo to the
cytosol with no effect on apoptosis. MTGM-induced mitochondrial fission can be blocked by a dominant
negative Drp1 mutant (Drp1-K38A). Overexpression of MTGM also results in inhibition of cell
proliferation, stalling of cells in S phase and nuclear accumulation of gamma-H2AX. Knockdown of
MTGM by RNA interference induces mitochondrial elongation, an increase of cell proliferation and
inhibition of cell death induced by apoptotic stimuli. In conclusion, MTGM is an
integral mitochondrial inner-membrane protein that coordinately regulates mitochondrial morphology
and cell proliferation (<a class='reflink' href='../../search/#ref11371'>Zhao <em>et al.</em> 2009</a>).&nbsp;</p>
<p><span class='highlight'>Romo1</span> is known to regulate <span class='highlight'>mitochondrial</span> ROS production and to act as an essential redox sensor in <span class='highlight'>mitochondrial</span> dynamics. &nbsp;<a class="reflink" href="/search/result.php?tc=1.A.111#ref34547928">Lee <em>et al.</em> 2018</a> reported that <span class='highlight'>Romo1</span> is a <span class='highlight'>mitochondrial</span> ion <span class='highlight'>channel</span> that differs from other identified ion channels. <span class='highlight'>Romo1</span> is highly conserved with structural features of class II viroporins (virus-encoded <span class='highlight'>nonselective</span> <span class='highlight'>cation</span> channels). Indeed, <span class='highlight'>Romo1</span> forms a <span class='highlight'>nonselective</span> <span class='highlight'>cation</span> <span class='highlight'>channel</span> with its amphipathic helical transmembrane domain necessary for pore-forming activity. C<span class='highlight'>hannel</span> activity was specifically inhibited by Fe<sup>2+</sup> ions, an essential transition metal ion in ROS metabolism. Using
structural bioinformatics, <a class="reflink" href="/search/result.php?tc=1.A.111#ref34547928">Lee <em>et al.</em> 2018</a> designed an experimental data-guided
structural model of <span class='highlight'>Romo1</span> with a rational hexameric structure. They proposed that <span class='highlight'>Romo1</span> establishes a new category of <span class='highlight'>viroporin-like</span> <span class='highlight'>nonselective</span> <span class='highlight'>cation</span> <span class='highlight'>channel</span>s in eukaryotes.</p></div>
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<div class="tcdb-fam-ref">
<h4>References associated with 1.A.111 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref34547928"></A>Lee, G.Y., D.G. You, H.R. Lee, S.W. Hwang, C.J. Lee, and Y. Do Yoo. (2018). Romo1 is a mitochondrial nonselective cation channel with viroporin-like characteristics. J. Cell Biol. [Epub: Ahead of Print] <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=29545371" target="_window">29545371</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34547927"></A>Zhao, J., T. Liu, S.B. Jin, N. Tomilin, J. Castro, O. Shupliakov, U. Lendahl, and M. Nistér. (2009). The novel conserved mitochondrial inner-membrane protein MTGM regulates mitochondrial morphology and cell proliferation. J Cell Sci 122: 2252-2262. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=19535734" target="_window">19535734</A></div>
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requirements/scraper/backup_files/TCFilesBackup/version__13h22m31s2832019/1.A.13.txt 0 → 100644
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<div class="next-level"><a href="/search/result.php?tc=1.A.13.6">View Proteins belonging to: <span style="color:maroon;">The Epithelial Chloride Channel (E-ClC) Family</span></a></div>
<!-- <div class="title">1.A.13: The Epithelial Chloride Channel (E-ClC) Family</div> -->
<div class="description"><p align='CENTER'><strong>1.A.13 The Epithelial Chloride Channel (E-ClC) Family </strong></p>
<p>Mammals have multiple isoforms (at least 6 different gene products plus splice variants (<a class="reflink" href="/search/result.php?tc=1.A.13#ref2984">Evans <em>et al</em>., 2004</a>)) of epithelial chloride channel proteins. The first member of this family to be characterized was a respiratory epithelium, Ca<sup>2+</sup>-regulated, chloride channel protein isolated from bovine tracheal apical membranes. It was biochemically characterized as a 140 kDa complex. The purified complex when reconstituted in a planar lipid bilayer behaved as an anion-selective channel. It was regulated by Ca<sup>2+</sup> via a calmodulin kinase II-dependent mechanism. When the cRNA was injected into <em>Xenopus</em> oocytes, an outward rectifying, DIDS-sensitive anion conductance was measured. A related gene, Lu-ECAM, was cloned from the bovine aortic endothelial cell line, BAEC. It is expressed in the lung and spleen but not in the trachea. Homologues are found in several mammals, and at least four paralogues (hCaCC-1-4) are present in humans, each with different tissue distributions.</p>
<p>The bovine EClC protein has 903 amino acids and four putative TMSs at residue positions 7-27, 331-351, 617-337 and 883-903. Distant (partial) homologues may be present in plants, ciliates and bacteria, <em>Synechocystis</em> (Sll0103; 420 aas) and <em>E. coli</em> (YfbK; 575 aas), so at least some domains within E-ClC family proteins have an ancient origin. E-ClC proteins show significant sequence similarity with CCA-&alpha;2&delta; family members (8.A.18).</p>
<p>Gibson et al. (<a class="reflink" href="/search/result.php?tc=1.A.13#ref3226">2005</a>) have shown that the human calcium-activated chloride channel, hCLCA1, is a secreted, non-integral membrane protein, and therefore suggest that this protein and its homologues are not ion channels at all. They also point out that the protein may not be sufficiently hydrophobic to insert into the membrane. Moreover, the proteins in subfamily 1.A.13.2 do not have &alpha;-TMSs, but hydrophilic domains in these proteins show sequence similarity to hydrophilic regions in proteins of family 8.A.18. The proteins without &alpha;-TMSs may not be channels. Thus, while some members of the E-ClC family appear to be able to form anion channels, others may not have this capacity.</p>
<p>The generalized reaction catalyzed by EClC family members is:</p>
<p align='CENTER'>Cl<sup>-</sup> (in) <img src='arrow.gif' alt='' /> Cl<sup>-</sup> (out)</p></div>
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<div class="tcdb-fam-ref">
<h4>References associated with 1.A.13 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref60"></A>Agnel, M., T. Vermat, and J. Culouscou. (1999). Identification of three novel members of the calcium-dependent chloride channel (CaCC) family predominantly expressed in the digestive tract and trachea. FEBS Lett. 455: 295-301. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=10437792" target="_window">10437792</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34547034"></A>Antonets, K.S., K.V. Volkov, A.L. Maltseva, L.M. Arshakian, A.P. Galkin, and A.A. Nizhnikov. (2016). Proteomic Analysis of <i>Escherichia coli</i> Protein Fractions Resistant to Solubilization by Ionic Detergents. Biochemistry (Mosc) 81: 34-46. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26885581" target="_window">26885581</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref61"></A>Barrett, K.E. and S.J. Keely. (2000). Chloride secretion by the intestinal epithelium: molecular basis and regulatory aspects. Annu. Rev. Physiol. 62: 535-572. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=10845102" target="_window">10845102</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref2204"></A>Elble, R.C., G. Ji, K. Nehrke, J. DeBiasio, P.D. Kingsley, M.I. Kotlikoff, and B.U. Pauli. (2002). Molecular and functional characterization of a murine calcium-activated chloride channel expressed in smooth muscle. J. Biol. Chem. 277: 18586-18591. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=11896056" target="_window">11896056</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref2984"></A>Evans, S.R., W.B. Thoreson, and C.L. Beck. (2004). Molecular and functional analyses of two new calcium-activated chloride channel family members from mouse eye and intestine. J. Biol. Chem. 279: 41792-41800. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=15284223" target="_window">15284223</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref59"></A>Fuller, C.M., I.I. Ismailov, D.A. Keeton, and D.J. Benos. (1994). Phosphorylation and activation of a bovine tracheal anion channel by Ca<sup>2+</sup>/calmodulin-dependent protein kinase II. J. Biol. Chem. 269: 26642-26650. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=7929397" target="_window">7929397</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref3226"></A>Gibson, A., A.P. Lewis, K. Affleck, A.J. Aitken, E. Meldrum, and N. Thompson. (2005). hCLCA1 and mCLCA3 are secreted non-integral membrane proteins and therefore are not ion channels. J. Biol. Chem. 280: 27205-27212. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=15919655" target="_window">15919655</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34545223"></A>Lee, R.M. and S.M. Jeong. (2016). [Identification of a Novel Calcium (Ca^(2+))-Activated Chloride Channel Accessory Gene in <i>Xenopus laevis</i>]. Mol Biol (Mosk) 50: 106-114. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=27028816" target="_window">27028816</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref8381"></A>Lee, R.M., R.H. Ryu, S.W. Jeong, S.J. Oh, H. Huang, J.S. Han, C.H. Lee, C.J. Lee, L.Y. Jan, and S.M. Jeong. (2011). Isolation and Expression Profile of the Ca-Activated Chloride Channel-like Membrane Protein 6 Gene in <i>Xenopus laevis</i>. Lab Anim Res 27: 109-116. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=21826170" target="_window">21826170</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref58"></A>Ran, S. and D.J. Benos. (1992). Immunopurification and structural analysis of a putative epithelial Cl<sup>-</sup> channel protein isolated from bovine trachea. J. Biol. Chem. 267: 3618-3625. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=1371273" target="_window">1371273</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref57"></A>Ran, S., C.M. Fuller, M. Pia Arrate, R. Latorre, and D.J. Benos. (1992). Functional reconstitution of a chloride channel protein from bovine trachea. J. Biol. Chem. 267: 20630-20637. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=1383206" target="_window">1383206</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34544933"></A>Sala-Rabanal, M., Z. Yurtsever, K.N. Berry, and T.J. Brett. (2015). Novel Roles for Chloride Channels, Exchangers, and Regulators in Chronic Inflammatory Airway Diseases. Mediators Inflamm 2015: 497387. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26612971" target="_window">26612971</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref5205"></A>Yoon, I.S., S.M. Jeong, S.N. Lee, J.H. Lee, J.H. Kim, M.K. Pyo, J.H. Lee, B.H. Lee, S.H. Choi, H. Rhim, H. Choe, and S.Y. Nah. (2006). Cloning and heterologous expression of a Ca<sup>2+</sup>-activated chloride channel isoform from rat brain. Biol Pharm Bull 29: 2168-2173. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=17077509" target="_window">17077509</A></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.14.5">View Proteins belonging to: <span style="color:maroon;">The Calcium Transporter A (CaTA) (formerly the Testis-Enhanced Gene Transfer (TEGT) Family</span></a></div>
<!-- <div class="title">1.A.14: The Calcium Transporter A (CaTA) (formerly the Testis-Enhanced Gene Transfer (TEGT) Family</div> -->
<div class="description"><p style='text-align: center;'><strong>1.A.14 The Calcium Transporter A (</strong><strong><strong>CaTA) </strong>(formerly the Testis-Enhanced Gene Transfer (TEGT)) Family</strong></p>
<p style='text-align: left;'>The CaTA family (also called the BI-1/YccA family; formerly the TEGT family (SwissProt family UPF0005;
Prosite entry PDOC00957)) includes members represented in all three
domains of life. One of these proteins, TEGT or the Bax Inhibitor-1 (TC#
1.A.14.1.1), has a C-terminal domain that forms a Ca<sup>2+</sup>-permeable channel (<a class='reflink' href='#ref8178'>Bultynck <em>et al.</em>, 2011</a>).&nbsp;
These proteins are about 200-250 residues in length and exhibit 7 TMSs.
They include the testis-enhanced gene transfer proteins of mammals
which are expressed at high levels in the testis, the putative
glutamate/aspartate binding proteins of plants and animals, the YccA
protein of <em>E. coli</em> and the YetJ protein of <em>Bacillus subtilis</em>.
They are distantly related to the ionotropic glutamate-binding protein
of the N-methyl D-aspartate (NMDA) receptor of man.&nbsp; Homologues include a
putative cold shock inducible protein and a SecY stabilizing protein (<a class='reflink' href='#ref8177'>van Stelten <em>et al.</em>, 2009</a>). Bacterial CaTA (BI-1) domains are found in 'fusion' proteins of&nbsp; histidine sensor kinases, diguanylate cyclases and proteins with ABC2-like P-loop ATPase domains. Transmembrane BAX Inhibitor-1 Motif-containing (TMBIM) proteins that mediate Ca<sup>2+</sup> homeostasis and cell
death have been reviewed (<a class="reflink" href="/search/result.php?tc=1.A.14#ref34546470">Liu 2017</a>).</p>
<p style='text-align: left;'>The Transmembrane BAX Inhibitor Motif containing (TMBIM) superfamily, divided into BAX Inhibitor (BI) and Lifeguard (LFG) families, comprises a group of cytoprotective cell death regulators conserved in prokaryotes and eukaryotes.&nbsp;<a class="reflink" href="/search/result.php?tc=1.A.14#ref34549313">Gamboa-Tuz <em>et al.</em> 2018</a> identified 685 TMBIM proteins in 171 organisms from Archaea, Bacteria, and Eukarya, and provided a phylogenetic overview of the whole TMBIM superfamily. A bacterial member of the CaTA family has been partially characterized. This is the YbhL protein of<em> E. coli</em>. It is 234 aas long, exhibits 7 putative TMSs and may stimulate glucose (and fructose?) uptake or metabolism in <em>E. coli</em>. It plays a role in preventing<em> E. coli</em> cell death in the stationary phase of growth (M. Inouye, personal communication).</p>
<p style='text-align: left;'>Homologues are found in a variety of Gram-negative and Gram-positive bacteria, yeast, fungi, plants, animals and viruses. The <em>E. coli </em>genome encodes three paralogues, YbhL, YbhM and YccA. Distant homologues found in <em>Drosophilia melanogaster</em> and the rat are the N-methyl-D-aspartate receptor-associated protein
(NMDARAI) (203 aas; pirS53708) and the N-methyl-D-aspartate receptor
glutamate binding chain (516 aas; pirS19586), respectively. Two others
are the rat neural membrane protein 35 (NMP35) (gbAF044201) and the <em>Arabidopsis thaliana</em> Bax inhibitor-1 (BI-1) protein capable of suppressing Bax-induced cell death in yeast (<em>S. cerevisiae</em>) (247 aas; gbAB025927). Most of the more closely related homologues of the<em> E. coli</em> SAD protein are of 200-250 aas.</p>
<p style='text-align: left;'>Bax Inhibitor-1 (BI-1) is an ER-localized protein that protects
against apoptosis and ER stress. BI-1 has been proposed to modulate ER
Ca<sup>2+</sup> homeostasis by acting as a Ca<sup>2+</sup>-leak channel. Based on experimental determination of the BI-1 topology, Bultynck et al. (<a class='reflink' href='#ref8178'>2011</a>) proposed that its C-terminal&nbsp;&alpha;-helical 20 aa peptide catalyzes Ca<sup>2+</sup> flux both <em>in vivo</em> and <em>in vitro</em>. The Ca<sup>2+</sup>-leak
properties were conserved among animal, but not plant and yeast
orthologs. By mutating one of the critical aspartate residues in the
proposed Ca<sup>2+</sup>-channel pore in full-length BI-1, D213 proved to be essential for BI-1 dependent ER Ca<sup>2+</sup>-leak.&nbsp;</p>
<p style='text-align: left;'>Calcium homeostasis balances passive calcium leak and active calcium
uptake. Human Bax inhibitor-1, BI-1, an antiapoptotic protein, is representative of a highly conserved and
widely distributed family, the transmembrane Bax inhibitor motif (TMBIM)
proteins. <a class='reflink' href='#ref11191'>Chang <em>et al.</em> 2014</a> published crystal structures of a bacterial homolog, YetJ (TC#
1.A.14.2.3) at 1.9&nbsp;&Aring; resolution
and characterized its calcium leak activity. Its
seven-transmembrane-helix fold features two triple-helix sandwiches
wrapped around a central C-terminal helix. Structures obtained in
closed and open conformations are reversibly interconvertible by changes
in the pH. A hydrogen-bonded perturbed pair of conserved aspartyl
residues explains the pH
dependence of this transition, and the pH
regulates calcium influx in proteoliposomes. Homology models for human
BI-1
provided insight into its cytoprotective
activity (<a class='reflink' href='#ref11191'>Chang <em>et al.</em> 2014</a>).&nbsp;</p>
<p style='text-align: left;'>GAAPs regulate Ca<sup>2+</sup> levels and fluxes from the Golgi and endoplasmic reticulum, confer resistance to a broad range of apoptotic stimuli, promote cell adhesion and migration via the activation of store- operated Ca<sup>2+</sup> entry, are essential for the viability of human cells, and affect orthopoxvirus virulence. GAAPs are oligomeric, multi-transmembrane proteins that form cation-selective ion channels that may explain the multiple functions of these proteins. Residues contributing to the ion-conducting pore have been defined and provide the first clues about the mechanistic link between these very different functions of GAAP. Although GAAPs are naturally oligomeric, they can also function as monomers (<a class="reflink" href="/search/result.php?tc=1.A.14#ref34546700">Carrara <em>et al.</em> 2017</a>).</p>
<p style='text-align: center;'>The generalized reaction catalyzed by TEGT channels is:</p>
<p style='text-align: center;'>Cations (out) ⇌ cations (in)</p></div>
<div class="next-level-result">
</div>
<div class="next-level"><a href="/search/result.php?tc=1.A.14.5">View Proteins belonging to: <span style="color:maroon;">The Calcium Transporter A (CaTA) (formerly the Testis-Enhanced Gene Transfer (TEGT) Family</span></a></div>
<div class="tcdb-fam-ref">
<h4>References associated with 1.A.14 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref8178"></A>Bultynck G., Kiviluoto S., Henke N., Ivanova H., Schneider L., Rybalchenko V., Luyten T., Nuyts K., De Borggraeve W., Bezprozvanny I., Parys JB., De Smedt H., Missiaen L. and Methner A. (2012). The C terminus of Bax inhibitor-1 forms a Ca2+-permeable channel pore. J Biol Chem. 287(4):2544-57. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=22128171" target="_window">22128171</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref8515"></A>Büttner, S., D. Ruli, F.N. Vögtle, L. Galluzzi, B. Moitzi, T. Eisenberg, O. Kepp, L. Habernig, D. Carmona-Gutierrez, P. Rockenfeller, P. Laun, M. Breitenbach, C. Khoury, K.U. Fröhlich, G. Rechberger, C. Meisinger, G. Kroemer, and F. Madeo. (2011). A yeast BH3-only protein mediates the mitochondrial pathway of apoptosis. EMBO. J. 30: 2779-2792. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=21673659" target="_window">21673659</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34543760"></A>Carrara G., Saraiva N., Parsons M., Byrne B., Prole DL., Taylor CW. and Smith GL. (2015). Golgi anti-apoptotic proteins are highly conserved ion channels that affect apoptosis and cell migration. J Biol Chem. 290(18):11785-801. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=25713081" target="_window">25713081</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546700"></A>Carrara, G., M. Parsons, N. Saraiva, and G.L. Smith. (2017). Golgi anti-apoptotic protein: a tale of camels, calcium, channels and cancer. Open Biol 7:. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=28469007" target="_window">28469007</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref11191"></A>Chang, Y., R. Bruni, B. Kloss, Z. Assur, E. Kloppmann, B. Rost, W.A. Hendrickson, and Q. Liu. (2014). Structural basis for a pH-sensitive calcium leak across membranes. Science 344: 1131-1135. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=24904158" target="_window">24904158</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34549313"></A>Gamboa-Tuz, S.D., A. Pereira-Santana, T. Zhao, M.E. Schranz, E. Castano, and L.C. Rodriguez-Zapata. (2018). New insights into the phylogeny of the TMBIM superfamily across the tree of life: Comparative genomics and synteny networks reveal independent evolution of the BI and LFG families in plants. Mol Phylogenet Evol 126: 266-278. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=29702215" target="_window">29702215</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34544804"></A>Jin, L., M. Miyazaki, S. Mizuno, M. Takigawa, T. Hirose, K. Nishimura, T. Toida, K. Williams, K. Kashiwagi, and K. Igarashi. (2008). The pore region of N-methyl-D-aspartate receptors differentially influences stimulation and block by spermine. J Pharmacol Exp Ther 327: 68-77. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=18632991" target="_window">18632991</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34544208"></A>Kota K., Kuzhikandathil EV., Afrasiabi M., Lacy B., Kontoyianni M., Crider AM. and Song D. (2015). Identification of key residues involved in the activation and signaling properties of dopamine D3 receptor. Pharmacol Res. 99:174-184. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=26116441" target="_window">26116441</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546470"></A>Liu, Q. (2017). TMBIM-mediated Ca<sup>2+</sup> homeostasis and cell death. Biochim. Biophys. Acta. [Epub: Ahead of Print] <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=28064000" target="_window">28064000</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34549265"></A>Luganini, A., G. Di Nardo, L. Munaron, G. Gilardi, A. Fiorio Pla, and G. Gribaudo. (2018). Human cytomegalovirus US21 protein is a viroporin that modulates calcium homeostasis and protects cells against apoptosis. Proc. Natl. Acad. Sci. USA 115: E12370-E12377. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=30530673" target="_window">30530673</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34546330"></A>M''Angale, P.G. and B.E. Staveley. (2016). Knockdown of the putative Lifeguard homologue CG3814 in neurons of <i>Drosophila melanogaster</i>. Genet Mol Res 15:. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=28002605" target="_window">28002605</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref8177"></A>van Stelten, J., F. Silva, D. Belin, and T.J. Silhavy. (2009). Effects of antibiotics and a proto-oncogene homolog on destruction of protein translocator SecY. Science 325: 753-756. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=19661432" target="_window">19661432</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34549424"></A>Yamagami, A., C. Saito, M. Nakazawa, S. Fujioka, T. Uemura, M. Matsui, M. Sakuta, K. Shinozaki, H. Osada, A. Nakano, T. Asami, and T. Nakano. (2017). Evolutionarily conserved BIL4 suppresses the degradation of brassinosteroid receptor BRI1 and regulates cell elongation. Sci Rep 7: 5739. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=28720789" target="_window">28720789</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref34547468"></A>Zhao, G.N., P. Zhang, J. Gong, X.J. Zhang, P.X. Wang, M. Yin, Z. Jiang, L.J. Shen, Y.X. Ji, J. Tong, Y. Wang, Q.F. Wei, Y. Wang, X.Y. Zhu, X. Zhang, J. Fang, Q. Xie, Z.G. She, Z. Wang, Z. Huang, and H. Li. (2017). Tmbim1 is a multivesicular body regulator that protects against non-alcoholic fatty liver disease in mice and monkeys by targeting the lysosomal degradation of Tlr4. Nat. Med. 23: 742-752. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=28481357" target="_window">28481357</A></div>
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<div class="next-level"><a href="/search/result.php?tc=1.A.15.2">View Proteins belonging to: <span style="color:maroon;">The Non-selective Cation Channel-2 (NSCC2) Family</span></a></div>
<!-- <div class="title">1.A.15: The Non-selective Cation Channel-2 (NSCC2) Family</div> -->
<div class="description"><p align='center'><strong>1.A.15 The Non-selective Cation Channel-2 (NSCC2) Family</strong></p>
<p align='justify'>Members of the NSCC2 family have been sequenced from various yeast, fungal and animals species including <em>Saccharomyces cerevisiae</em>, <em>Drosophila melanogaster</em> and <em>Homo sapiens</em>. These proteins are the Sec62 proteins, believed to be associated with the Sec61 and Sec63 constituents of the general protein secretory systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins have been implicated in platelet derived growth factor (PDGF)-dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. The channels are reported to exhibit equal selectivity for Na<sup>+</sup><sup> </sup>, K<sup>+</sup><sup> </sup> and Cs<sup>+</sup><sup> </sup> with low permeability to Ca<sup>2+&nbsp;</sup>, and no permeability to anions. Channel open probability is voltage- and cytoplasmic Ca<sup>2+</sup>-independent.</p>
<p align='justify'>Sequenced NSCC2 family proteins are 283-402 amino acyl residues in length and exhibit two putative transmembrane &alpha;-helical spanners (TMSs). The <em>S. cerevisiae</em> protein, of 283 amino acyl residues, has cytoplasmic N- and C-termini with two putative TMSs at positions 159-178 and 193-213. The C-terminal 25 residues are rich in arginine and lysine. The animal proteins are about 30% identical to the yeast proteins. It is not known if the yeast proteins can function as ion channels or if the animal proteins facilitate protein secretion. These proteins have been reported to be present in both endoplasmic reticular and cytoplasmic membranes. In spite of their observed low Ca<sup>2+&nbsp;</sup> conductance, the mammalian NSCC2 proteins are irreversibly activated by maitotoxin (MTX). MTX may also form pores at higher concentrations (<a class='reflink' href='#ref4859'>Egido <em>et al</em>., 2008</a>). NSCC2 channels are believed<sup>&nbsp;</sup>to provide&nbsp;entry pathways in response to growth factors.</p>
<p>The generalized transport reaction catalyzed by members of the NSCC2 family is:</p>
<p align='center'>Cation (out) <img src='arrow.gif' alt='' /> cation (in)</p></div>
<div class="next-level-result">
</div>
<div class="next-level"><a href="/search/result.php?tc=1.A.15.2">View Proteins belonging to: <span style="color:maroon;">The Non-selective Cation Channel-2 (NSCC2) Family</span></a></div>
<div class="tcdb-fam-ref">
<h4>References associated with 1.A.15 family:</h4>
<div class="ref">
<div class=''>
<A ID="ref4859"></A><a id="ref4859"></a><a id="ref4859"></a>Egido, W., V. Castrejón, B. Antón, and M. Martínez. (2008). Maitotoxin induces two dose-dependent conductances in <em>Xenopus oocytes</em>. Comparison with nystatin effects as a pore inductor. Toxicon. 51: 797-812. <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&amp;term=18255116" target="_window">18255116</a> <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&amp;term=18255116" target="_window">18255116</a> <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=18255116" target="_window">18255116</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref69"></A><a id="ref69"></a>Bihler, H., C.L. Slayman, and A. Bertl. (1998). NSC1: a novel high-current inward rectifier for cations in the plasma membrane of <em>Saccharomyces cerevisiae</em>. FEBS Lett. 432: 59-64. <a href="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&amp;term=9710251" target="_window">9710251</a> <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=9710251" target="_window">9710251</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref67"></A>Estacion, M., H. B. Nguyen and J.J. Gargus (1996). Calcium is permeable through a maitotoxin-activated nonselective cation channel in mouse L cells. Am. J. Physiol. 270: C1145-C1152. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=8928742" target="_window">8928742</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref68"></A>Fantino, E., D. Church, U. Bengtsson and J.J. Gargus (1997). Mammalian gene encoding growth factor-activated cation channel is homologue to yeast microsomal protein SEC62 and maps to human chromosome 3. J. Gen. Physiol. 110: 44a. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=" target="_window"></A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref64"></A>Frace, A.M. and J.J. Gargus (1989). Activation of single-channel currents in mouse fibroblasts by platelet-derived growth factor. Proc. Natl. Acad. Sci. USA 86: 2511-2515. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=2467305" target="_window">2467305</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref65"></A>Gargus, J.J., A.M. Frace and F. Jung (1993). The role of a PDGF-activated nonselective cation channel in the proliferative response. <I>In</I> &quot;Nonselective cation channels: pharmacology, physiology and biophysics&quot; (D. Siemen and J. Hescheler, eds.), Birkh&auml;user Verlag, Basel, Switzerland, pp. 289-295. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=7505659" target="_window">7505659</A></div>
</div>
<div class="ref">
<div class=''>
<A ID="ref66"></A>Jung, F., S. Selvaraj and J.J. Gargus (1992). Blockers of platelet-derived growth factor-activated nonselective cation channel inhibit cell proliferation. Am. J. Physiol. 262: C1464-C1470. <A HREF="http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&term=1377445" target="_window">1377445</A></div>
</div>
<div class="ref">
<div class=''>
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