This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

1uw8

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 12:30, 11 September 2015

CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE

Structural highlights

1uw8 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:	,
Related:	1j58, 1l3j
Activity:	Oxalate decarboxylase, with EC number 4.1.1.2
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

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

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/1uw8"

@@ Line 2: / Line 2: @@
 <StructureSection load='1uw8' size='340' side='right' caption='[[1uw8]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1uw8]] is a 1 chain structure with 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=1UW8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UW8 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1uw8]] 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=1UW8 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UW8 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1j58|1j58]], [[1l3j|1l3j]]</td></tr>
 <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Oxalate_decarboxylase Oxalate decarboxylase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1uw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uw8 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uw8 RCSB], [http://www.ebi.ac.uk/pdbsum/1uw8 PDBsum]</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=1uw8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uw8 OCA], [http://pdbe.org/1uw8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uw8 RCSB], [http://www.ebi.ac.uk/pdbsum/1uw8 PDBsum]</span></td></tr>
 </table>
 == Function ==
@@ Line 28: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1uw8" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Bacillus subtilis]]
+[[Category: Bacillus globigii migula 1900]]
 [[Category: Oxalate decarboxylase]]
 [[Category: Bornemann, S]]

1uw8

From Proteopedia

Revision as of 12:30, 11 September 2015

CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox