5v4o - Revision history

OCA at 09:14, 25 October 2023

OCA — Wed, 25 Oct 2023 09:14:43 GMT

←Older revision		Revision as of 09:14, 25 October 2023
Line 4:		Line 4:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5v4o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V4O FirstGlance]. <br>		<table><tr><td colspan='2'>[[5v4o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V4O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TOX:1-HYDROPEROXY-L-TRYPTOPHAN'>TOX</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]] 1.95Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TOX:1-HYDROPEROXY-L-TRYPTOPHAN'>TOX</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=5v4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v4o OCA], [https://pdbe.org/5v4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v4o RCSB], [https://www.ebi.ac.uk/pdbsum/5v4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v4o 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=5v4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v4o OCA], [https://pdbe.org/5v4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v4o RCSB], [https://www.ebi.ac.uk/pdbsum/5v4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v4o ProSAT]</span></td></tr>
	</table>		</table>

OCA at 12:01, 1 February 2023

OCA — Wed, 01 Feb 2023 12:01:56 GMT

←Older revision		Revision as of 12:01, 1 February 2023
Line 3:		Line 3:
	<StructureSection load='5v4o' size='340' side='right'caption='[[5v4o]], [[Resolution\|resolution]] 1.95Å' scene=''>		<StructureSection load='5v4o' size='340' side='right'caption='[[5v4o]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v4o]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Burp1 Burp1~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V4O OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5V4O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v4o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5V4O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>~~</td></tr>~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=TOX:1-HYDROPEROXY-L-TRYPTOPHAN'>TOX</scene></td></tr>
-	~~<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat">~~<scene name='pdbligand=TOX:1-HYDROPEROXY-L-TRYPTOPHAN'>TOX</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=5v4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v4o OCA], [https://pdbe.org/5v4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5v4o RCSB], [https://www.ebi.ac.uk/pdbsum/5v4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5v4o ProSAT]</span></td></tr>
-	~~<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v53\|5v53]]</td></tr>~~	+
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">katG, BURPS1710b_3366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 BURP1])</td></tr>	+
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase_peroxidase Catalase peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.21 1.11.1.21] </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=5v4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v4o OCA], [~~http~~://pdbe.org/5v4o PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5v4o RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5v4o PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5v4o ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/KATG_BURP1 KATG_BURP1]] Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity.	+	[https://www.uniprot.org/uniprot/KATG_BURP1 KATG_BURP1] Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 29:		Line 25:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Burp1]]~~	+	[[Category: Burkholderia pseudomallei 1710b]]
-	~~[[Category: Catalase peroxidase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Loewen~~, P C]]~~	+	[[Category: Loewen PC]]
-	~~[[Category: Catalase]]~~	+
-	~~[[Category: D141a/q233e/n240d]]~~	+
-	~~[[Category: Heme]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Peroxidase~~]]	+

OCA at 08:30, 30 September 2020

OCA — Wed, 30 Sep 2020 08:30:58 GMT

←Older revision		Revision as of 08:30, 30 September 2020
Line 1:		Line 1:

	==Crystal structure of the D141A/Q233E/N240D variant of catalase-peroxidase from B. pseudomallei==		==Crystal structure of the D141A/Q233E/N240D variant of catalase-peroxidase from B. pseudomallei==
-	<StructureSection load='5v4o' size='340' side='right' caption='[[5v4o]], [[Resolution\|resolution]] 1.95Å' scene=''>	+	<StructureSection load='5v4o' size='340' side='right'caption='[[5v4o]], [[Resolution\|resolution]] 1.95Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5v4o]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V4O OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5V4O FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5v4o]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burp1 Burp1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V4O OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5V4O FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TOX:1-HYDROPEROXY-L-TRYPTOPHAN'>TOX</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TOX:1-HYDROPEROXY-L-TRYPTOPHAN'>TOX</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v53\|5v53]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v53\|5v53]]</td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">katG, BURPS1710b_3366 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=320372 BURP1])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase_peroxidase Catalase peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.21 1.11.1.21] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase_peroxidase Catalase peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.21 1.11.1.21] </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=5v4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v4o OCA], [http://pdbe.org/5v4o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v4o RCSB], [http://www.ebi.ac.uk/pdbsum/5v4o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v4o 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=5v4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v4o OCA], [http://pdbe.org/5v4o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v4o RCSB], [http://www.ebi.ac.uk/pdbsum/5v4o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v4o ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 21:		Line 22:
	</div>		</div>
	<div class="pdbe-citations 5v4o" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5v4o" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Catalase 3D structures\|Catalase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Burp1]]
	[[Category: Catalase peroxidase]]		[[Category: Catalase peroxidase]]
		+	[[Category: Large Structures]]
	[[Category: Loewen, P C]]		[[Category: Loewen, P C]]
	[[Category: Catalase]]		[[Category: Catalase]]

OCA at 13:54, 27 April 2017

OCA — Thu, 27 Apr 2017 13:54:19 GMT

←Older revision		Revision as of 13:54, 27 April 2017
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5v4o is ~~ON HOLD until Paper~~ Publication	+	==Crystal structure of the D141A/Q233E/N240D variant of catalase-peroxidase from B. pseudomallei==
		+	<StructureSection load='5v4o' size='340' side='right' caption='[[5v4o]], [[Resolution\|resolution]] 1.95Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5v4o]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5V4O OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5V4O FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=TOX:1-HYDROPEROXY-L-TRYPTOPHAN'>TOX</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5v53\|5v53]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase_peroxidase Catalase peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.21 1.11.1.21] </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=5v4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5v4o OCA], [http://pdbe.org/5v4o PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5v4o RCSB], [http://www.ebi.ac.uk/pdbsum/5v4o PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5v4o ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/KATG_BURP1 KATG_BURP1]] Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The unusual Met-Tyr-Trp adduct composed of cross-linked side chains along with an associated mobile Arg is essential for catalase activity in catalase-peroxidases. In addition, acidic residues in the entrance channel, in particular an Asp and a Glu approximately 7 and approximately 15 A, respectively, from the heme, significantly enhance catalase activity. The mechanism by which these channel carboxylates influence catalase activity is the focus of this work. Seventeen new variants with fewer and additional acidic residues have been constructed and characterized structurally and for enzymatic activity, revealing that their effect on activity is roughly inversely proportional to their distance from the heme and adduct, suggesting that the electrostatic potential of the heme cavity may be affected. A discrete group of protonable residues are contained within a 15 A sphere surrounding the heme iron, and a computational analysis reveals that the pKa of the distal His112, alone, is modulated within the pH range of catalase activity by the remote acidic residues in a pattern consistent with its protonated form having a key role in the catalase reaction cycle. The electrostatic potential also impacts the catalatic reaction through its influence on the charged status of the Met-Tyr-Trp adduct.

-	~~Authors: Loewen, P~~.C.	+	The Catalase Activity of Catalase-Peroxidases Is Modulated by Changes in the pKa of the Distal Histidine.,Machuqueiro M, Victor B, Switala J, Villanueva J, Rovira C, Fita I, Loewen PC Biochemistry. 2017 Apr 20. doi: 10.1021/acs.biochem.6b01276. PMID:28409923<ref>PMID:28409923</ref>

-	~~Description: Crystal structure~~ of the ~~D141A/Q233E/N240D variant~~ of ~~catalase-peroxidase from B~~. ~~pseudomallei~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
-	[[Category: Loewen, P.C]]	+	<div class="pdbe-citations 5v4o" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Catalase peroxidase]]
		+	[[Category: Loewen, P C]]
		+	[[Category: Catalase]]
		+	[[Category: D141a/q233e/n240d]]
		+	[[Category: Heme]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Peroxidase]]

OCA: Protected "5v4o" [edit=sysop:move=sysop]

OCA — Wed, 05 Apr 2017 11:35:15 GMT

Protected "5v4o" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:35, 5 April 2017

OCA: New page: '''Unreleased structure''' The entry 5v4o is ON HOLD until Paper Publication Authors: Loewen, P.C. Description: Crystal structure of the D141A/Q233E/N240D variant of catalase-peroxidas...

OCA — Wed, 05 Apr 2017 11:35:13 GMT

New page: '''Unreleased structure''' The entry 5v4o is ON HOLD until Paper Publication Authors: Loewen, P.C. Description: Crystal structure of the D141A/Q233E/N240D variant of catalase-peroxidas...

New page

'''Unreleased structure'''

The entry 5v4o is ON HOLD until Paper Publication

Authors: Loewen, P.C.

Description: Crystal structure of the D141A/Q233E/N240D variant of catalase-peroxidase from B. pseudomallei
[[Category: Unreleased Structures]]
[[Category: Loewen, P.C]]