1l3j

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[[Image:1l3j.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of Oxalate Decarboxylase Formate Complex==
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|PDB= 1l3j |SIZE=350|CAPTION= <scene name='initialview01'>1l3j</scene>, resolution 1.90&Aring;
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<StructureSection load='1l3j' size='340' side='right'caption='[[1l3j]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene> and <scene name='pdbligand=FMT:FORMIC ACID'>FMT</scene>
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<table><tr><td colspan='2'>[[1l3j]] 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=1L3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1L3J FirstGlance]. <br>
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|ACTIVITY=
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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]] 1.9&#8491;</td></tr>
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|GENE= yvrK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])
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<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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
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}}
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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=1l3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l3j OCA], [https://pdbe.org/1l3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1l3j RCSB], [https://www.ebi.ac.uk/pdbsum/1l3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1l3j ProSAT]</span></td></tr>
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</table>
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'''Crystal Structure of Oxalate Decarboxylase Formate Complex'''
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== Function ==
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[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.
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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Oxalate decarboxylase is a manganese-dependent enzyme that catalyzes the conversion of oxalate to formate and carbon dioxide. We have determined the structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution in the presence of formate. The structure reveals a hexamer with 32-point symmetry in which each monomer belongs to the cupin family of proteins. Oxalate decarboxylase is further classified as a bicupin because it contains two cupin folds, possibly resulting from gene duplication. Each oxalate decarboxylase cupin domain contains one manganese binding site. Each of the oxalate decarboxylase domains is structurally similar to oxalate oxidase, which catalyzes the manganese-dependent oxidative decarboxylation of oxalate to carbon dioxide and hydrogen peroxide. Amino acid side chains in the two metal binding sites of oxalate decarboxylase and the metal binding site of oxalate oxidase are very similar. Four manganese binding residues (three histidines and one glutamate) are conserved as well as a number of hydrophobic residues. The most notable difference is the presence of Glu333 in the metal binding site of the second cupin domain of oxalate decarboxylase. We postulate that this domain is responsible for the decarboxylase activity and that Glu333 serves as a proton donor in the production of formate. Mutation of Glu333 to alanine reduces the catalytic activity by a factor of 25. The function of the other domain in oxalate decarboxylase is not yet known.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l3/1l3j_consurf.spt"</scriptWhenChecked>
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1L3J is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1L3J OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution., Anand R, Dorrestein PC, Kinsland C, Begley TP, Ealick SE, Biochemistry. 2002 Jun 18;41(24):7659-69. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12056897 12056897]
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1l3j ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Anand, R.]]
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[[Category: Anand R]]
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[[Category: Begley, T P.]]
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[[Category: Begley TP]]
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[[Category: Dorrestein, P C.]]
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[[Category: Dorrestein PC]]
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[[Category: Ealick, S E.]]
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[[Category: Ealick SE]]
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[[Category: Kinsland, C.]]
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[[Category: Kinsland C]]
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[[Category: FMT]]
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[[Category: MG]]
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[[Category: MN]]
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[[Category: cupin]]
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[[Category: decarboxylase]]
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[[Category: formate]]
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[[Category: manganese]]
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[[Category: oxalate]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:25:50 2008''
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Current revision

Crystal Structure of Oxalate Decarboxylase Formate Complex

PDB ID 1l3j

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