3s0m - Revision history

OCA at 09:46, 1 March 2024

OCA — Fri, 01 Mar 2024 09:46:44 GMT

←Older revision		Revision as of 09:46, 1 March 2024
Line 3:		Line 3:
	<StructureSection load='3s0m' size='340' side='right'caption='[[3s0m]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='3s0m' size='340' side='right'caption='[[3s0m]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s0m]] 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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s0m]] 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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S0M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</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]] 2.31Å</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]]</div></td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, yvrK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [https://pdbe.org/3s0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [https://www.ebi.ac.uk/pdbsum/3s0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s0m 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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [https://pdbe.org/3s0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [https://www.ebi.ac.uk/pdbsum/3s0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s0m 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.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	The conformational properties of an active-site loop segment, defined by residues Ser(161)-Glu(162)-Asn(163)-Ser(164), have been shown to be important for modulating the intrinsic reactivity of Mn(II) in the active site of Bacillus subtilis oxalate decarboxylase. We now detail the functional and structural consequences of removing a conserved Arg/Thr hydrogen-bonding interaction by site-specific mutagenesis. Hence, substitution of Thr-165 by a valine residue gives an OxDC variant (T165V) that exhibits impaired catalytic activity. Heavy-atom isotope effect measurements, in combination with the X-ray crystal structure of the T165V OxDC variant, demonstrate that the conserved Arg/Thr hydrogen bond is important for correctly locating the side chain of Glu-162, which mediates a proton-coupled electron transfer (PCET) step prior to decarboxylation in the catalytically competent form of OxDC. In addition, we show that the T165V OxDC variant exhibits a lower level of oxalate consumption per dioxygen molecule, consistent with the predictions of recent spin-trapping experiments [Imaram et al. (2011) Free Radicals Biol. Med. 50, 1009-1015]. This finding implies that dioxygen might participate as a reversible electron sink in two putative PCET steps and is not merely used to generate a protein-based radical or oxidized metal center.	+
-		+
-	A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.,Saylor BT, Reinhardt LA, Lu Z, Shukla MS, Nguyen L, Cleland WW, Angerhofer A, Allen KN, Richards NG Biochemistry. 2012 Apr 3;51(13):2911-20. Epub 2012 Mar 19. PMID:22404040<ref>PMID:22404040</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 3s0m" style="background-color:#fffaf0;"></div>~~	+
-	~~== References ==~~	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Vibrio~~ subtilis ~~ehrenberg 1835~~]]	+	[[Category: Bacillus subtilis]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Oxalate decarboxylase]]~~	+	[[Category: Allen KN]]
-	[[Category: Allen~~, K N~~]]	+	[[Category: Cleland WW]]
-	[[Category: Cleland~~, W W~~]]	+	[[Category: Lu Z]]
-	[[Category: Lu, Z]]	+	[[Category: Reinhardt LA]]
-	[[Category: Reinhardt~~, L A~~]]	+	[[Category: Richards NGJ]]
-	[[Category: Richards~~, N G.J~~]]	+	[[Category: Saylor BT]]
-	[[Category: Saylor~~, B T~~]]	+	[[Category: Shukla MS]]
-	[[Category: Shukla~~, M S]]~~	+
-	~~[[Category: Bicupin]]~~	+
-	~~[[Category: Lyase~~]]	+

OCA at 10:32, 22 June 2022

OCA — Wed, 22 Jun 2022 10:32:51 GMT

←Older revision		Revision as of 10:32, 22 June 2022
Line 1:		Line 1:

	==A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase==		==A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase==
-	<StructureSection load='3s0m' size='340' side='right' caption='[[3s0m]], [[Resolution\|resolution]] 2.31Å' scene=''>	+	<StructureSection load='3s0m' size='340' side='right'caption='[[3s0m]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s0m]] is a 1 chain structure with sequence from [~~http~~://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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3S0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s0m]] 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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3S0M FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j58\|1j58]]</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]]</div></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, yvrK ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, yvrK ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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='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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [~~http~~://pdbe.org/3s0m PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/3s0m PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=3s0m 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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [https://pdbe.org/3s0m PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [https://www.ebi.ac.uk/pdbsum/3s0m PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3s0m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 26:		Line 26:
	</StructureSection>		</StructureSection>
	[[Category: Vibrio subtilis ehrenberg 1835]]		[[Category: Vibrio subtilis ehrenberg 1835]]
		+	[[Category: Large Structures]]
	[[Category: Oxalate decarboxylase]]		[[Category: Oxalate decarboxylase]]
	[[Category: Allen, K N]]		[[Category: Allen, K N]]

OCA at 09:31, 8 November 2017

OCA — Wed, 08 Nov 2017 09:31:31 GMT

←Older revision		Revision as of 09:31, 8 November 2017
Line 3:		Line 3:
	<StructureSection load='3s0m' size='340' side='right' caption='[[3s0m]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='3s0m' size='340' side='right' caption='[[3s0m]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s0m]] 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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s0m]] is a 1 chain structure with sequence from [http://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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S0M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j58\|1j58]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j58\|1j58]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, yvrK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</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='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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [http://pdbe.org/3s0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [http://www.ebi.ac.uk/pdbsum/3s0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s0m ProSAT]</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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [http://pdbe.org/3s0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [http://www.ebi.ac.uk/pdbsum/3s0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s0m ProSAT]</span></td></tr>
Line 25:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus globigii migula 1900~~]]	+	[[Category: Vibrio subtilis ehrenberg 1835]]
	[[Category: Oxalate decarboxylase]]		[[Category: Oxalate decarboxylase]]
	[[Category: Allen, K N]]		[[Category: Allen, K N]]

OCA at 23:06, 5 August 2016

OCA — Fri, 05 Aug 2016 23:06:32 GMT

←Older revision		Revision as of 23:06, 5 August 2016
Line 1:		Line 1:
		+
	==A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase==		==A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase==
	<StructureSection load='3s0m' size='340' side='right' caption='[[3s0m]], [[Resolution\|resolution]] 2.31Å' scene=''>		<StructureSection load='3s0m' size='340' side='right' caption='[[3s0m]], [[Resolution\|resolution]] 2.31Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[3s0m]] 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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S0M FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[3s0m]] 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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S0M FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j58\|1j58]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j58\|1j58]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, yvrK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus ~~subtilis~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, 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='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='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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [http://www.ebi.ac.uk/pdbsum/3s0m 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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [http://pdbe.org/3s0m PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [http://www.ebi.ac.uk/pdbsum/3s0m PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3s0m ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 19:		Line 20:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 3s0m" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Bacillus ~~subtilis~~]]	+	[[Category: Bacillus globigii migula 1900]]
	[[Category: Oxalate decarboxylase]]		[[Category: Oxalate decarboxylase]]
	[[Category: Allen, K N]]		[[Category: Allen, K N]]

OCA at 22:43, 25 December 2014

OCA — Thu, 25 Dec 2014 22:43:46 GMT

←Older revision		Revision as of 22:43, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[3s0m]] 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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S0M FirstGlance]. <br>		<table><tr><td colspan='2'>[[3s0m]] 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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S0M FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j58\|1j58]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j58\|1j58]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, yvrK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, yvrK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
-	<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [http://www.ebi.ac.uk/pdbsum/3s0m 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=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [http://www.ebi.ac.uk/pdbsum/3s0m PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 15:		Line 17:
	A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.,Saylor BT, Reinhardt LA, Lu Z, Shukla MS, Nguyen L, Cleland WW, Angerhofer A, Allen KN, Richards NG Biochemistry. 2012 Apr 3;51(13):2911-20. Epub 2012 Mar 19. PMID:22404040<ref>PMID:22404040</ref>		A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.,Saylor BT, Reinhardt LA, Lu Z, Shukla MS, Nguyen L, Cleland WW, Angerhofer A, Allen KN, Richards NG Biochemistry. 2012 Apr 3;51(13):2911-20. Epub 2012 Mar 19. PMID:22404040<ref>PMID:22404040</ref>

-	From ~~MEDLINEÂ®~~/~~PubMedÂ®~~, a database of the U.S. National Library of Medicine.<br>	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
	== References ==		== References ==
Line 23:		Line 25:
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Oxalate decarboxylase]]		[[Category: Oxalate decarboxylase]]
-	[[Category: Allen, K N.]]	+	[[Category: Allen, K N]]
-	[[Category: Cleland, W W.]]	+	[[Category: Cleland, W W]]
-	[[Category: Lu, Z.]]	+	[[Category: Lu, Z]]
-	[[Category: Reinhardt, L A.]]	+	[[Category: Reinhardt, L A]]
-	[[Category: Richards, N G.J.]]	+	[[Category: Richards, N G.J]]
-	[[Category: Saylor, B T.]]	+	[[Category: Saylor, B T]]
-	[[Category: Shukla, M S.]]	+	[[Category: Shukla, M S]]
	[[Category: Bicupin]]		[[Category: Bicupin]]
	[[Category: Lyase]]		[[Category: Lyase]]

OCA at 04:45, 5 June 2014

OCA — Thu, 05 Jun 2014 04:45:53 GMT

←Older revision		Revision as of 04:45, 5 June 2014
Line 1:		Line 1:
-	[[~~Image:~~3s0m.~~jpg~~\|~~left~~\|~~200px~~]]	+	==A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase==
		+	<StructureSection load='3s0m' size='340' side='right' caption='[[3s0m]], [[Resolution\|resolution]] 2.31Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[3s0m]] 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=3S0M OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3S0M FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CO3:CARBONATE+ION'>CO3</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j58\|1j58]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">BSU33240, oxalate decarboxylase, oxdC, yvrK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3s0m FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3s0m OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3s0m RCSB], [http://www.ebi.ac.uk/pdbsum/3s0m PDBsum]</span></td></tr>
		+	<table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The conformational properties of an active-site loop segment, defined by residues Ser(161)-Glu(162)-Asn(163)-Ser(164), have been shown to be important for modulating the intrinsic reactivity of Mn(II) in the active site of Bacillus subtilis oxalate decarboxylase. We now detail the functional and structural consequences of removing a conserved Arg/Thr hydrogen-bonding interaction by site-specific mutagenesis. Hence, substitution of Thr-165 by a valine residue gives an OxDC variant (T165V) that exhibits impaired catalytic activity. Heavy-atom isotope effect measurements, in combination with the X-ray crystal structure of the T165V OxDC variant, demonstrate that the conserved Arg/Thr hydrogen bond is important for correctly locating the side chain of Glu-162, which mediates a proton-coupled electron transfer (PCET) step prior to decarboxylation in the catalytically competent form of OxDC. In addition, we show that the T165V OxDC variant exhibits a lower level of oxalate consumption per dioxygen molecule, consistent with the predictions of recent spin-trapping experiments [Imaram et al. (2011) Free Radicals Biol. Med. 50, 1009-1015]. This finding implies that dioxygen might participate as a reversible electron sink in two putative PCET steps and is not merely used to generate a protein-based radical or oxidized metal center.

-	<!--	+	A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.,Saylor BT, Reinhardt LA, Lu Z, Shukla MS, Nguyen L, Cleland WW, Angerhofer A, Allen KN, Richards NG Biochemistry. 2012 Apr 3;51(13):2911-20. Epub 2012 Mar 19. PMID:22404040<ref>PMID:22404040</ref>
-	~~The line below this paragraph~~, ~~containing "STRUCTURE_3s0m"~~, ~~creates the "Structure Box" on the page~~.	+
-	~~You may change the PDB parameter~~ (~~which sets the PDB file loaded into the applet~~)	+
-	~~or the SCENE parameter (which sets the initial scene displayed when the page is loaded),~~	+
-	~~or leave the SCENE parameter empty for the default display.~~	+
-	-->	+
-	~~{{STRUCTURE_3s0m\| PDB=3s0m \| SCENE= }}~~	+

-	~~===A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase===~~	+	From MEDLINEÂ®/PubMedÂ®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-		+	== References ==
-	~~<!--~~	+	<references/>
-	~~The line below this paragraph~~, ~~{{ABSTRACT_PUBMED_22404040}}, adds~~ the ~~Publication Abstract to the page~~	+	__TOC__
-	~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 22404040 is the PubMed ID number~~.	+	</StructureSection>
-	-->	+
-	~~{{ABSTRACT_PUBMED_22404040}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[3s0m]] 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=3S0M OCA].~~	+
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:022404040<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Bacillus subtilis]]		[[Category: Bacillus subtilis]]
	[[Category: Oxalate decarboxylase]]		[[Category: Oxalate decarboxylase]]

OCA at 09:12, 25 April 2012

OCA — Wed, 25 Apr 2012 09:12:42 GMT

←Older revision		Revision as of 09:12, 25 April 2012
Line 1:		Line 1:
-	~~'''Unreleased structure'''~~	+	[[Image:3s0m.jpg\|left\|200px]]

-	The ~~entry 3s0m~~ is ~~ON HOLD~~ ~~until Paper Publication~~	+	<!--
		+	The line below this paragraph, containing "STRUCTURE_3s0m", creates the "Structure Box" on the page.
		+	You may change the PDB parameter (which sets the PDB file loaded into the applet)
		+	or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
		+	or leave the SCENE parameter empty for the default display.
		+	-->
		+	{{STRUCTURE_3s0m\| PDB=3s0m \| SCENE= }}

-	~~Authors: Saylor, B.T., Reinhardt, L.~~A~~., Lu, Z., Shukla, M.S., Cleland, W.W., Allen, K.N., Richards, N.G.J.~~	+	===A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase===

-	~~Description~~: ~~A Structural Element that Modulates Proton~~-~~Coupled Electron Transfer in~~ Oxalate ~~Decarboxylase~~	+
		+	<!--
		+	The line below this paragraph, {{ABSTRACT_PUBMED_22404040}}, adds the Publication Abstract to the page
		+	(as it appears on PubMed at http://www.pubmed.gov), where 22404040 is the PubMed ID number.
		+	-->
		+	{{ABSTRACT_PUBMED_22404040}}
		+
		+	==About this Structure==
		+	[[3s0m]] 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=3S0M OCA].
		+
		+	==Reference==
		+	<ref group="xtra">PMID:022404040</ref><references group="xtra"/>
		+	[[Category: Bacillus subtilis]]
		+	[[Category: Oxalate decarboxylase]]
		+	[[Category: Allen, K N.]]
		+	[[Category: Cleland, W W.]]
		+	[[Category: Lu, Z.]]
		+	[[Category: Reinhardt, L A.]]
		+	[[Category: Richards, N G.J.]]
		+	[[Category: Saylor, B T.]]
		+	[[Category: Shukla, M S.]]
		+	[[Category: Bicupin]]
		+	[[Category: Lyase]]

OCA at 11:43, 16 November 2011

OCA — Wed, 16 Nov 2011 11:43:07 GMT

←Older revision		Revision as of 11:43, 16 November 2011
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 3s0m is ON HOLD	+	The entry 3s0m is ON HOLD until Paper Publication

	Authors: Saylor, B.T., Reinhardt, L.A., Lu, Z., Shukla, M.S., Cleland, W.W., Allen, K.N., Richards, N.G.J.		Authors: Saylor, B.T., Reinhardt, L.A., Lu, Z., Shukla, M.S., Cleland, W.W., Allen, K.N., Richards, N.G.J.

-	Description: ~~Something about the T165V OxDC mutant~~	+	Description: A Structural Element that Modulates Proton-Coupled Electron Transfer in Oxalate Decarboxylase

OCA at 04:51, 8 June 2011

OCA — Wed, 08 Jun 2011 04:51:50 GMT

←Older revision		Revision as of 04:51, 8 June 2011
Line 3:		Line 3:
	The entry 3s0m is ON HOLD		The entry 3s0m is ON HOLD

-	Authors: Saylor, ~~Benjamin~~ T., Reinhardt, ~~Laurie~~ A., Lu, ~~Zhibing~~, Shukla, ~~Mithila~~ S., Cleland, W. ~~Wallace~~, Allen, ~~Karen~~ N., Richards, ~~Nigel~~ G.J.	+	Authors: Saylor, B.T., Reinhardt, L.A., Lu, Z., Shukla, M.S., Cleland, W.W., Allen, K.N., Richards, N.G.J.

	Description: Something about the T165V OxDC mutant		Description: Something about the T165V OxDC mutant

OCA: Protected "3s0m" [edit=sysop:move=sysop]

OCA — Wed, 25 May 2011 05:12:34 GMT

Protected "3s0m" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:12, 25 May 2011