1l3j

From Proteopedia

(Difference between revisions)

Revision as of 07:54, 25 November 2020

Crystal Structure of Oxalate Decarboxylase Formate Complex

Structural highlights

1l3j is a 1 chain structure with sequence from "bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Gene:	yvrK ("Bacillus globigii" Migula 1900)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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 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.

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:12056897^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Anand R, Dorrestein PC, Kinsland C, Begley TP, Ealick SE. Structure of oxalate decarboxylase from Bacillus subtilis at 1.75 A resolution. Biochemistry. 2002 Jun 18;41(24):7659-69. PMID:12056897

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1l3j"

@@ Line 1: / Line 1: @@
 ==Crystal Structure of Oxalate Decarboxylase Formate Complex==
-<StructureSection load='1l3j' size='340' side='right' caption='[[1l3j]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1l3j' size='340' side='right'caption='[[1l3j]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1l3j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1L3J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1l3j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. 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 [http://proteopedia.org/fgij/fg.htm?mol=1L3J FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yvrK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=1l3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l3j OCA], [http://pdbe.org/1l3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l3j RCSB], [http://www.ebi.ac.uk/pdbsum/1l3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l3j ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1l3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1l3j OCA], [http://pdbe.org/1l3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1l3j RCSB], [http://www.ebi.ac.uk/pdbsum/1l3j PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1l3j ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 14: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l3/1l3j_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/l3/1l3j_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 34: / Line 34: @@
 </StructureSection>
 [[Category: Bacillus globigii migula 1900]]
+[[Category: Large Structures]]
 [[Category: Anand, R]]
 [[Category: Begley, T P]]

1l3j

From Proteopedia

Revision as of 07:54, 25 November 2020

Crystal Structure of Oxalate Decarboxylase Formate Complex

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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