5j4i: Difference between revisions

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'''Unreleased structure'''


The entry 5j4i is ON HOLD  until Paper Publication
==Crystal Structure of the L-arginine/agmatine antiporter from E. coli at 2.2 Angstroem resolution==
<StructureSection load='5j4i' size='340' side='right'caption='[[5j4i]], [[Resolution|resolution]] 2.21&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5j4i]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_O157:H7 Escherichia coli O157:H7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J4I FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.207&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5j4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4i OCA], [https://pdbe.org/5j4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j4i RCSB], [https://www.ebi.ac.uk/pdbsum/5j4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4i ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/ADIC_ECOLI ADIC_ECOLI] Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach (Probable). Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons (PubMed:12867448, PubMed:14594828, PubMed:19578361, PubMed:21368142). Probably undergoes several conformational states in order to translocate the substrate across the membrane; keeps the substrate accessible to only 1 side of the membrane at a time by opening and closing 3 membrane-internal gates (Probable).<ref>PMID:12867448</ref> <ref>PMID:14594828</ref> <ref>PMID:19578361</ref> <ref>PMID:21368142</ref> <ref>PMID:14594828</ref> <ref>PMID:21368142</ref>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Pathogenic enterobacteria need to survive the extreme acidity of the stomach to successfully colonize the human gut. Enteric bacteria circumvent the gastric acid barrier by activating extreme acid-resistance responses, such as the arginine-dependent acid resistance system. In this response, l-arginine is decarboxylated to agmatine, thereby consuming one proton from the cytoplasm. In Escherichia coli, the l-arginine/agmatine antiporter AdiC facilitates the export of agmatine in exchange of l-arginine, thus providing substrates for further removal of protons from the cytoplasm and balancing the intracellular pH. We have solved the crystal structures of wild-type AdiC in the presence and absence of the substrate agmatine at 2.6-A and 2.2-A resolution, respectively. The high-resolution structures made possible the identification of crucial water molecules in the substrate-binding sites, unveiling their functional roles for agmatine release and structure stabilization, which was further corroborated by molecular dynamics simulations. Structural analysis combined with site-directed mutagenesis and the scintillation proximity radioligand binding assay improved our understanding of substrate binding and specificity of the wild-type l-arginine/agmatine antiporter AdiC. Finally, we present a potential mechanism for conformational changes of the AdiC transport cycle involved in the release of agmatine into the periplasmic space of E. coli.


Authors:  
Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.,Ilgu H, Jeckelmann JM, Gapsys V, Ucurum Z, de Groot BL, Fotiadis D Proc Natl Acad Sci U S A. 2016 Aug 31. pii: 201605442. PMID:27582465<ref>PMID:27582465</ref>


Description:  
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 5j4i" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Escherichia coli O157:H7]]
[[Category: Large Structures]]
[[Category: Fotiadis D]]
[[Category: Ilgue H]]
[[Category: Jeckelmann JM]]
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