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| | <StructureSection load='2uyb' size='340' side='right'caption='[[2uyb]], [[Resolution|resolution]] 2.10Å' scene=''> | | <StructureSection load='2uyb' size='340' side='right'caption='[[2uyb]], [[Resolution|resolution]] 2.10Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2uyb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UYB FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2uyb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2UYB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UYB FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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]] 2.1Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j58|1j58]], [[1l3j|1l3j]], [[1uw8|1uw8]], [[2uy9|2uy9]], [[2uya|2uya]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Oxalate_decarboxylase Oxalate decarboxylase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.2 4.1.1.2] </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=2uyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uyb OCA], [https://pdbe.org/2uyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uyb RCSB], [https://www.ebi.ac.uk/pdbsum/2uyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uyb 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=2uyb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uyb OCA], [https://pdbe.org/2uyb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uyb RCSB], [https://www.ebi.ac.uk/pdbsum/2uyb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uyb ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[https://www.uniprot.org/uniprot/OXDC_BACSU OXDC_BACSU]] Converts oxalate to formate and CO(2) in an O(2)-dependent reaction. Can also catalyze minor side reactions: oxalate oxidation to produce H(2)O(2), and oxalate-dependent, H(2)O(2)-independent dye oxidations.
| + | [https://www.uniprot.org/uniprot/OXDC_BACSU OXDC_BACSU] Converts oxalate to formate and CO(2) in an O(2)-dependent reaction. Can also catalyze minor side reactions: oxalate oxidation to produce H(2)O(2), and oxalate-dependent, H(2)O(2)-independent dye oxidations. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Vibrio subtilis ehrenberg 1835]] | + | [[Category: Bacillus subtilis]] |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Oxalate decarboxylase]]
| + | [[Category: Bornemann S]] |
| - | [[Category: Bornemann, S]] | + | [[Category: Bowater L]] |
| - | [[Category: Bowater, L]] | + | [[Category: Burrell MR]] |
| - | [[Category: Burrell, M R]] | + | [[Category: Just VJ]] |
| - | [[Category: Just, V J]] | + | [[Category: Lawson DM]] |
| - | [[Category: Lawson, D M]] | + | [[Category: McRobbie I]] |
| - | [[Category: McRobbie, I]] | + | [[Category: Stevenson CEM]] |
| - | [[Category: Stevenson, C E.M]] | + | |
| - | [[Category: Cupin]]
| + | |
| - | [[Category: Decarboxylase]]
| + | |
| - | [[Category: Formate]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Manganese]]
| + | |
| - | [[Category: Metal binding protein]]
| + | |
| - | [[Category: Metal-binding]]
| + | |
| - | [[Category: Oxalate]]
| + | |
| - | [[Category: S161a mutant]]
| + | |
| Structural highlights
Function
OXDC_BACSU Converts oxalate to formate and CO(2) in an O(2)-dependent reaction. Can also catalyze minor side reactions: oxalate oxidation to produce H(2)O(2), and oxalate-dependent, H(2)O(2)-independent dye oxidations.
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
Oxalate decarboxylase (EC 4.1.1.2) catalyses the conversion of oxalate into carbon dioxide and formate. It requires manganese and, uniquely, dioxygen for catalysis. It forms a homohexamer and each subunit contains two similar, but distinct, manganese sites termed sites 1 and 2. There is kinetic evidence that only site 1 is catalytically active and that site 2 is purely structural. However, the kinetics of enzymes with mutations in site 2 are often ambiguous and all mutant kinetics have been interpreted without structural information. Nine new site-directed mutants have been generated and four mutant crystal structures have now been solved. Most mutants targeted (i) the flexibility (T165P), (ii) favoured conformation (S161A, S164A, D297A or H299A) or (iii) presence (Delta162-163 or Delta162-164) of a lid associated with site 1. The kinetics of these mutants were consistent with only site 1 being catalytically active. This was particularly striking with D297A and H299A because they disrupted hydrogen bonds between the lid and a neighbouring subunit only when in the open conformation and were distant from site 2. These observations also provided the first evidence that the flexibility and stability of lid conformations are important in catalysis. The deletion of the lid to mimic the plant oxalate oxidase led to a loss of decarboxylase activity, but only a slight elevation in the oxalate oxidase side reaction, implying other changes are required to afford a reaction specificity switch. The four mutant crystal structures (R92A, E162A, Delta162-163 and S161A) strongly support the hypothesis that site 2 is purely structural.
The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations.,Just VJ, Burrell MR, Bowater L, McRobbie I, Stevenson CE, Lawson DM, Bornemann S Biochem J. 2007 Nov 1;407(3):397-406. PMID:17680775[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Just VJ, Burrell MR, Bowater L, McRobbie I, Stevenson CE, Lawson DM, Bornemann S. The identity of the active site of oxalate decarboxylase and the importance of the stability of active-site lid conformations. Biochem J. 2007 Nov 1;407(3):397-406. PMID:17680775 doi:10.1042/BJ20070708
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