This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

5j4n

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Current revision

Crystal structure of the L-arginine/agmatine antiporter AdiC in complex with agmatine at 2.6 Angstroem resolution

Structural highlights

5j4n is a 2 chain structure with sequence from Escherichia coli O157:H7. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.594Å
Ligands:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

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.

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^[7]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Gong S, Richard H, Foster JW. YjdE (AdiC) is the arginine:agmatine antiporter essential for arginine-dependent acid resistance in Escherichia coli. J Bacteriol. 2003 Aug;185(15):4402-9. PMID:12867448 doi:10.1128/JB.185.15.4402-4409.2003
↑ Iyer R, Williams C, Miller C. Arginine-agmatine antiporter in extreme acid resistance in Escherichia coli. J Bacteriol. 2003 Nov;185(22):6556-61. PMID:14594828 doi:10.1128/JB.185.22.6556-6561.2003
↑ Fang Y, Jayaram H, Shane T, Kolmakova-Partensky L, Wu F, Williams C, Xiong Y, Miller C. Structure of a prokaryotic virtual proton pump at 3.2 A resolution. Nature. 2009 Aug 20;460(7258):1040-3. Epub 2009 Jul 5. PMID:19578361 doi:10.1038/nature08201
↑ Kowalczyk L, Ratera M, Paladino A, Bartoccioni P, Errasti-Murugarren E, Valencia E, Portella G, Bial S, Zorzano A, Fita I, Orozco M, Carpena X, Vazquez-Ibar JL, Palacin M. Molecular basis of substrate-induced permeation by an amino acid antiporter. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3935-40. Epub 2011 Feb 22. PMID:21368142 doi:10.1073/pnas.1018081108
↑ Iyer R, Williams C, Miller C. Arginine-agmatine antiporter in extreme acid resistance in Escherichia coli. J Bacteriol. 2003 Nov;185(22):6556-61. PMID:14594828 doi:10.1128/JB.185.22.6556-6561.2003
↑ Kowalczyk L, Ratera M, Paladino A, Bartoccioni P, Errasti-Murugarren E, Valencia E, Portella G, Bial S, Zorzano A, Fita I, Orozco M, Carpena X, Vazquez-Ibar JL, Palacin M. Molecular basis of substrate-induced permeation by an amino acid antiporter. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3935-40. Epub 2011 Feb 22. PMID:21368142 doi:10.1073/pnas.1018081108
↑ Ilgu H, Jeckelmann JM, Gapsys V, Ucurum Z, de Groot BL, Fotiadis D. Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proc Natl Acad Sci U S A. 2016 Aug 31. pii: 201605442. PMID:27582465 doi:http://dx.doi.org/10.1073/pnas.1605442113

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5j4n"

Categories: Escherichia coli O157:H7 | Large Structures | Fotiadis D | Ilgue H | Jeckelmann JM

@@ Line 3: / Line 3: @@
 <StructureSection load='5j4n' size='340' side='right'caption='[[5j4n]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5j4n]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Eco57 Eco57]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5J4N OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5J4N FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5j4n]] 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=5J4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5J4N FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.594&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adiC, Z5717, ECs5097 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83334 ECO57])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG2:AGMATINE'>AG2</scene></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5j4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4n OCA], [http://pdbe.org/5j4n PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5j4n RCSB], [http://www.ebi.ac.uk/pdbsum/5j4n PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4n ProSAT]</span></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=5j4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5j4n OCA], [https://pdbe.org/5j4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5j4n RCSB], [https://www.ebi.ac.uk/pdbsum/5j4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5j4n ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ADIC_ECO57 ADIC_ECO57]] Major component of the acid-resistance (AR) system allowing enteric pathogens to survive the acidic environment in the stomach. Exchanges extracellular arginine for its intracellular decarboxylation product agmatine (Agm) thereby expelling intracellular protons.
+[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 ==
@@ Line 23: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Eco57]]
+[[Category: Escherichia coli O157:H7]]
 [[Category: Large Structures]]
-[[Category: Fotiadis, D]]
+[[Category: Fotiadis D]]
-[[Category: Ilgue, H]]
+[[Category: Ilgue H]]
-[[Category: Jeckelmann, J M]]
+[[Category: Jeckelmann JM]]
-[[Category: Adic-agmatine complex]]
-[[Category: Exchanger]]
-[[Category: Membrane protein]]
-[[Category: Transport protein]]
-[[Category: Transporter]]

5j4n

From Proteopedia

Current revision

Crystal structure of the L-arginine/agmatine antiporter AdiC in complex with agmatine at 2.6 Angstroem resolution

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox