6cz9

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Current revision (14:31, 13 March 2024) (edit) (undo)
 
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<StructureSection load='6cz9' size='340' side='right'caption='[[6cz9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='6cz9' size='340' side='right'caption='[[6cz9]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[6cz9]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/'shewanella_trabarsenatis' 'shewanella trabarsenatis']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZ9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6CZ9 FirstGlance]. <br>
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<table><tr><td colspan='2'>[[6cz9]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Shewanella_sp._ANA-3 Shewanella sp. ANA-3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6CZ9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6CZ9 FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AST:ARSENITE'>AST</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=MO:MOLYBDENUM+ATOM'>MO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG5:1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE'>PG5</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">arrA, Shewana3_2341 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=94122 'Shewanella trabarsenatis']), arrB, Shewana3_2340 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=94122 'Shewanella trabarsenatis'])</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AST:ARSENITE'>AST</scene>, <scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MGD:2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE+GUANOSINE+DINUCLEOTIDE'>MGD</scene>, <scene name='pdbligand=MO:MOLYBDENUM+ATOM'>MO</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG5:1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE'>PG5</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6cz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cz9 OCA], [http://pdbe.org/6cz9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6cz9 RCSB], [http://www.ebi.ac.uk/pdbsum/6cz9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6cz9 ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6cz9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6cz9 OCA], [https://pdbe.org/6cz9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6cz9 RCSB], [https://www.ebi.ac.uk/pdbsum/6cz9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6cz9 ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/ARRA_SHESA ARRA_SHESA] Component of the arsenate respiratory reductase (Arr) complex, which catalyzes the reduction of arsenate (As(V)) to arsenite (As(III)) (PubMed:12939408, PubMed:17951391, PubMed:30104376). ArrA is the arsenate-binding subunit (PubMed:30104376). The periplasmic localization of this complex may allow the cell to couple arsenate reduction to energy production before arsenate can be transported to the cell cytoplasm and enter the ars detoxification pathway, an energy-requiring process (PubMed:17951391).<ref>PMID:12939408</ref> <ref>PMID:17951391</ref> <ref>PMID:30104376</ref>
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Arsenate respiration by bacteria was discovered over two decades ago and is catalyzed by diverse organisms using the well-conserved Arr enzyme complex. Until now, the mechanisms underpinning this metabolism have been relatively opaque. Here, we report the structure of an Arr complex (solved by X-ray crystallography to 1.6-A resolution), which was enabled by an improved Arr expression method in the genetically tractable arsenate respirer Shewanella sp. ANA-3. We also obtained structures bound with the substrate arsenate (1.8 A), the product arsenite (1.8 A), and the natural inhibitor phosphate (1.7 A). The structures reveal a conserved active-site motif that distinguishes Arr [(R/K)GRY] from the closely related arsenite respiratory oxidase (Arx) complex (XGRGWG). Arr activity assays using methyl viologen as the electron donor and arsenate as the electron acceptor display two-site ping-pong kinetics. A Mo(V) species was detected with EPR spectroscopy, which is typical for proteins with a pyranopterin guanine dinucleotide cofactor. Arr is an extraordinarily fast enzyme that approaches the diffusion limit (Km = 44.6 +/- 1.6 muM, kcat = 9,810 +/- 220 seconds(-1)), and phosphate is a competitive inhibitor of arsenate reduction (Ki = 325 +/- 12 muM). These observations, combined with knowledge of typical sedimentary arsenate and phosphate concentrations and known rates of arsenate desorption from minerals in the presence of phosphate, suggest that (i) arsenate desorption limits microbiologically induced arsenate reductive mobilization and (ii) phosphate enhances arsenic mobility by stimulating arsenate desorption rather than by inhibiting it at the enzymatic level.
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Structural and mechanistic analysis of the arsenate respiratory reductase provides insight into environmental arsenic transformations.,Glasser NR, Oyala PH, Osborne TH, Santini JM, Newman DK Proc Natl Acad Sci U S A. 2018 Aug 13. pii: 1807984115. doi:, 10.1073/pnas.1807984115. PMID:30104376<ref>PMID:30104376</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 6cz9" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Shewanella trabarsenatis]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Glasser, N R]]
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[[Category: Shewanella sp. ANA-3]]
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[[Category: Newman, D K]]
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[[Category: Glasser NR]]
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[[Category: Arsenate]]
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[[Category: Newman DK]]
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[[Category: Arsenite]]
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[[Category: Molybdoprotein]]
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[[Category: Molybdopterin]]
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[[Category: Oxidoreductase]]
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Current revision

The arsenate respiratory reductase (Arr) complex from Shewanella sp. ANA-3 bound to arsenite

PDB ID 6cz9

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