3ob6

From Proteopedia

(Difference between revisions)

Current revision

Structure of AdiC(N101A) in the open-to-out Arg+ bound conformation

Structural highlights

3ob6 is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3Å
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

Transporters of the amino acid, polyamine and organocation (APC) superfamily play essential roles in cell redox balance, cancer, and aminoacidurias. The bacterial L-arginine/agmatine antiporter, AdiC, is the main APC structural paradigm and shares the "5 + 5 inverted repeat" fold found in other families like the Na(+)-coupled neurotransmitter transporters. The available AdiC crystal structures capture two states of its transport cycle: the open-to-out apo and the outward-facing Arg(+)-bound occluded. However, the role of Arg(+) during the transition between these two states remains unknown. Here, we report the crystal structure at 3.0 A resolution of an Arg(+)-bound AdiC mutant (N101A) in the open-to-out conformation, completing the picture of the major conformational states during the transport cycle of the 5 + 5 inverted repeat fold-transporters. The N101A structure is an intermediate state between the previous known AdiC conformations. The Arg(+)-guanidinium group in the current structure presents high mobility and delocalization, hampering substrate occlusion and resulting in a low translocation rate. Further analysis supports that proper coordination of this group with residues Asn101 and Trp293 is required to transit to the occluded state, providing the first clues on the molecular mechanism of substrate-induced fit in a 5 + 5 inverted repeat fold-transporter. The pseudosymmetry found between repeats in AdiC, and in all fold-related transporters, restraints the conformational changes, in particular the transmembrane helices rearrangements, which occur during the transport cycle. In AdiC these movements take place away from the dimer interface, explaining the independent functioning of each subunit.

Molecular basis of substrate-induced permeation by an amino acid antiporter.,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 Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):3935-40. Epub 2011 Feb 22. PMID:21368142^[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
↑ 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

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/3ob6"

@@ Line 3: / Line 3: @@
 <StructureSection load='3ob6' size='340' side='right'caption='[[3ob6]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3ob6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OB6 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3ob6]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OB6 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OB6 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</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]] 3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">adiC, B21_03947 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 "Bacillus coli" Migula 1895])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ARG:ARGININE'>ARG</scene></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=3ob6 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ob6 OCA], [https://pdbe.org/3ob6 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ob6 RCSB], [https://www.ebi.ac.uk/pdbsum/3ob6 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ob6 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 ==
@@ Line 21: / Line 23: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus coli migula 1895]]
+[[Category: Escherichia coli]]
 [[Category: Large Structures]]
-[[Category: Carpena, X]]
+[[Category: Carpena X]]
-[[Category: Fita, I]]
+[[Category: Fita I]]
-[[Category: Kowalczyk, L]]
+[[Category: Kowalczyk L]]
-[[Category: Palacin, M]]
+[[Category: Palacin M]]
-[[Category: Ratera, M]]
+[[Category: Ratera M]]
-[[Category: Valencia, E]]
+[[Category: Valencia E]]
-[[Category: Vazquez-lbar, J L]]
+[[Category: Vazquez-lbar JL]]
-[[Category: 5+5 inverted repeat]]
-[[Category: Amino acid antiporter]]
-[[Category: Apc-t]]
-[[Category: Arginine]]
-[[Category: Membrane]]
-[[Category: Membrane protein]]
-[[Category: Transmembrane antiporter]]

3ob6

From Proteopedia

Current revision

Structure of AdiC(N101A) in the open-to-out Arg+ bound conformation

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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