We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

1uw8

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (13:01, 13 December 2023) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1uw8.gif|left|200px]]<br />
 
-
<applet load="1uw8" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1uw8, resolution 2.00&Aring;" />
 
-
'''CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE'''<br />
 
-
==Overview==
+
==CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE==
-
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.
+
<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 [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='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</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='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>
 +
== 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.
 +
== Evolutionary Conservation ==
 +
[[Image:Consurf_key_small.gif|200px|right]]
 +
Check<jmol>
 +
<jmolCheckbox>
 +
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uw/1uw8_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</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=1uw8 ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== 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.
-
==About this Structure==
+
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<ref>PMID:14871895</ref>
-
1UW8 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with MN and TRS as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1UW8 OCA].
+
-
==Reference==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14871895 14871895]
+
</div>
 +
<div class="pdbe-citations 1uw8" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
 +
__TOC__
 +
</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
-
[[Category: Oxalate decarboxylase]]
+
[[Category: Large Structures]]
-
[[Category: Single protein]]
+
[[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: MN]]
+
-
[[Category: TRS]]
+
-
[[Category: cupin]]
+
-
[[Category: decarboxylase]]
+
-
[[Category: formate]]
+
-
[[Category: lyase]]
+
-
[[Category: manganese]]
+
-
[[Category: metal binding protein]]
+
-
[[Category: oxalate]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 17:13:24 2007''
+

Current revision

CRYSTAL STRUCTURE OF OXALATE DECARBOXYLASE

PDB ID 1uw8

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1uw8"
Personal tools