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| | ==Crystal Structure of the Reaction Intermediate between Pyruvate oxidase containing FAD and TPP, and Substrate Pyruvate== | | ==Crystal Structure of the Reaction Intermediate between Pyruvate oxidase containing FAD and TPP, and Substrate Pyruvate== |
| - | <StructureSection load='1v5g' size='340' side='right' caption='[[1v5g]], [[Resolution|resolution]] 1.96Å' scene=''> | + | <StructureSection load='1v5g' size='340' side='right'caption='[[1v5g]], [[Resolution|resolution]] 1.96Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1v5g]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Aerococcus_viridans Aerococcus viridans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V5G OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V5G FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1v5g]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Aerococcus_viridans Aerococcus viridans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V5G OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V5G FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HTL:2-ACETYL-THIAMINE+DIPHOSPHATE'>HTL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 1.96Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pox|1pox]], [[1v5e|1v5e]], [[1v5f|1v5f]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=HTL:2-ACETYL-THIAMINE+DIPHOSPHATE'>HTL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Pyruvate_oxidase Pyruvate oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.3.3 1.2.3.3] </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=1v5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v5g OCA], [https://pdbe.org/1v5g PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v5g RCSB], [https://www.ebi.ac.uk/pdbsum/1v5g PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v5g ProSAT]</span></td></tr> |
| - | <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=1v5g FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v5g OCA], [http://pdbe.org/1v5g PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v5g RCSB], [http://www.ebi.ac.uk/pdbsum/1v5g PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v5g ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Aerococcus viridans]] | | [[Category: Aerococcus viridans]] |
| - | [[Category: Pyruvate oxidase]] | + | [[Category: Large Structures]] |
| - | [[Category: Hossain, M T]] | + | [[Category: Hossain MT]] |
| - | [[Category: Imamura, S]] | + | [[Category: Imamura S]] |
| - | [[Category: Sekiguchi, T]] | + | [[Category: Sekiguchi T]] |
| - | [[Category: Suzuki, K]] | + | [[Category: Suzuki K]] |
| - | [[Category: Takenaka, A]] | + | [[Category: Takenaka A]] |
| - | [[Category: Yamamoto, T]] | + | [[Category: Yamamoto T]] |
| - | [[Category: Flavoprotein]]
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| - | [[Category: Oxidoreductase]]
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| Structural highlights
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The crystal structures of pyruvate oxidase from Aerococcus viridans (AvPOX) complexed with flavin adenine dinucleotide (FAD), with FAD and thiamine diphosphate (ThDP) and with FAD and the 2-acetyl-ThDP intermediate (AcThDP) have been determined at 1.6, 1.8 and 1.9 A resolution, respectively. Each subunit of the homotetrameric AvPOX enzyme consists of three domains, as observed in other ThDP-dependent enzymes. FAD is bound within one subunit in the elongated conformation and with the flavin moiety being planar in the oxidized form, while ThDP is bound in a conserved V-conformation at the subunit-subunit interface. The structures reveal flexible regions in the active-site tunnel which may undergo conformational changes to allow the entrance of the substrates and the exit of the reaction products. Of particular interest is the role of Lys478, the side chain of which may be bent or extended depending on the stage of catalysis. The structures also provide insight into the routes for electron transfer to FAD and the involvement of active-site residues in the catalysis of pyruvate to its products.
The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis.,Juan EC, Hoque MM, Hossain MT, Yamamoto T, Imamura S, Suzuki K, Sekiguchi T, Takenaka A Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Nov 1;63(Pt, 11):900-7. Epub 2007 Oct 20. PMID:18007037[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Juan EC, Hoque MM, Hossain MT, Yamamoto T, Imamura S, Suzuki K, Sekiguchi T, Takenaka A. The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2007 Nov 1;63(Pt, 11):900-7. Epub 2007 Oct 20. PMID:18007037 doi:10.1107/S1744309107041012
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