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| | <StructureSection load='1uw8' size='340' side='right'caption='[[1uw8]], [[Resolution|resolution]] 2.00Å' scene=''> | | <StructureSection load='1uw8' size='340' side='right'caption='[[1uw8]], [[Resolution|resolution]] 2.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1uw8]] 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=1UW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UW8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1uw8]] 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=1UW8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UW8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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]] 2Å</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]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=1uw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uw8 OCA], [https://pdbe.org/1uw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uw8 RCSB], [https://www.ebi.ac.uk/pdbsum/1uw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uw8 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=1uw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uw8 OCA], [https://pdbe.org/1uw8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uw8 RCSB], [https://www.ebi.ac.uk/pdbsum/1uw8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uw8 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: Just VJ]] |
| - | [[Category: Just, V J]] | + | [[Category: Lawson DM]] |
| - | [[Category: Lawson, D M]] | + | [[Category: Stevenson CEM]] |
| - | [[Category: Stevenson, C E.M]] | + | [[Category: Tanner A]] |
| - | [[Category: Tanner, A]] | + | |
| - | [[Category: Cupin]]
| + | |
| - | [[Category: Decarboxylase]]
| + | |
| - | [[Category: Formate]]
| + | |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Manganese]]
| + | |
| - | [[Category: Metal binding protein]]
| + | |
| - | [[Category: Oxalate]]
| + | |
| 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) catalyzes the conversion of oxalate to formate and carbon dioxide and utilizes dioxygen as a cofactor. By contrast, the evolutionarily related oxalate oxidase (EC 1.2.3.4) converts oxalate and dioxygen to carbon dioxide and hydrogen peroxide. Divergent free radical catalytic mechanisms have been proposed for these enzymes that involve the requirement of an active site proton donor in the decarboxylase but not the oxidase reaction. The oxidase possesses only one domain and manganese binding site per subunit, while the decarboxylase has two domains and two manganese sites per subunit. A structure of the decarboxylase together with a limited mutagenesis study has recently been interpreted as evidence that the C-terminal domain manganese binding site (site 2) is the catalytic site and that Glu-333 is the crucial proton donor (Anand, R., Dorrestein, P. C., Kinsland, C., Begley, T. P., and Ealick, S. E. (2002) Biochemistry 41, 7659-7669). The N-terminal binding site (site 1) of this structure is solvent-exposed (open) and lacks a suitable proton donor for the decarboxylase reaction. We report a new structure of the decarboxylase that shows a loop containing a 3(10) helix near site 1 in an alternative conformation. This loop adopts a "closed" conformation forming a lid covering the entrance to site 1. This conformational change brings Glu-162 close to the manganese ion, making it a new candidate for the crucial proton donor. Site-directed mutagenesis of equivalent residues in each domain provides evidence that Glu-162 performs this vital role and that the N-terminal domain is either the sole or the dominant catalytically active domain.
A closed conformation of Bacillus subtilis oxalate decarboxylase OxdC provides evidence for the true identity of the active site.,Just VJ, Stevenson CE, Bowater L, Tanner A, Lawson DM, Bornemann S J Biol Chem. 2004 May 7;279(19):19867-74. Epub 2004 Feb 10. PMID:14871895[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Just VJ, Stevenson CE, Bowater L, Tanner A, Lawson DM, Bornemann S. A closed conformation of Bacillus subtilis oxalate decarboxylase OxdC provides evidence for the true identity of the active site. J Biol Chem. 2004 May 7;279(19):19867-74. Epub 2004 Feb 10. PMID:14871895 doi:10.1074/jbc.M313820200
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