5sx3 - Revision history

OCA at 12:49, 4 October 2023

2023-10-04T12:49:52Z

←Older revision		Revision as of 12:49, 4 October 2023
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	<StructureSection load='5sx3' size='340' side='right'caption='[[5sx3]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='5sx3' size='340' side='right'caption='[[5sx3]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5sx3]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Burp1 Burp1~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fxg 2fxg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SX3 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5SX3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5sx3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Burkholderia_pseudomallei_1710b Burkholderia pseudomallei 1710b]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fxg 2fxg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SX3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SX3 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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~~></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]] 2Å</td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l02\|5l02]], [[5l05\|5l05]], [[5sw4\|5sw4]], [[5sw5\|5sw5]], [[5sw6\|5sw6]], [[5sx0\|5sx0]], [[5sx1\|5sx1]], [[5sx2\|5sx2]], [[5sx6\|5sx6]], [[5sx7\|5sx7]], [[5sxq\|5sxq]], [[5sxr\|5sxr]], [[5sxs\|5sxs]], [[5sxt\|5sxt]], [[5sxx\|5sxx]], [[5syh\|5syh]], [[5syi\|5syi]], [[5syj\|5syj]], [[5syk\|5syk]], [[5syl\|5syl]], [[5syu\|5syu]], [[5syv\|5syv]], [[5syw\|5syw]], [[5syx\|5syx]], [[5syy\|5syy]]</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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></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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5sx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sx3 OCA], [https://pdbe.org/5sx3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5sx3 RCSB], [https://www.ebi.ac.uk/pdbsum/5sx3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5sx3 ProSAT]</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=5sx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sx3 OCA], [~~http~~://pdbe.org/5sx3 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5sx3 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5sx3 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5sx3 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 ==
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	__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-peroxidase]]~~	+
-	~~[[Category: Katg]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Ph change~~]]	+

OCA at 08:13, 8 January 2020

2020-01-08T08:13:46Z

←Older revision		Revision as of 08:13, 8 January 2020
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	==Crystal structure of the catalase-peroxidase KatG of B. pseudomaallei at pH 4.5==		==Crystal structure of the catalase-peroxidase KatG of B. pseudomaallei at pH 4.5==
-	<StructureSection load='5sx3' size='340' side='right' caption='[[5sx3]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='5sx3' size='340' side='right'caption='[[5sx3]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5sx3]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fxg 2fxg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SX3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SX3 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5sx3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Burp1 Burp1]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fxg 2fxg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SX3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SX3 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l02\|5l02]], [[5l05\|5l05]], [[5sw4\|5sw4]], [[5sw5\|5sw5]], [[5sw6\|5sw6]], [[5sx0\|5sx0]], [[5sx1\|5sx1]], [[5sx2\|5sx2]], [[5sx6\|5sx6]], [[5sx7\|5sx7]], [[5sxq\|5sxq]], [[5sxr\|5sxr]], [[5sxs\|5sxs]], [[5sxt\|5sxt]], [[5sxx\|5sxx]], [[5syh\|5syh]], [[5syi\|5syi]], [[5syj\|5syj]], [[5syk\|5syk]], [[5syl\|5syl]], [[5syu\|5syu]], [[5syv\|5syv]], [[5syw\|5syw]], [[5syx\|5syx]], [[5syy\|5syy]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5l02\|5l02]], [[5l05\|5l05]], [[5sw4\|5sw4]], [[5sw5\|5sw5]], [[5sw6\|5sw6]], [[5sx0\|5sx0]], [[5sx1\|5sx1]], [[5sx2\|5sx2]], [[5sx6\|5sx6]], [[5sx7\|5sx7]], [[5sxq\|5sxq]], [[5sxr\|5sxr]], [[5sxs\|5sxs]], [[5sxt\|5sxt]], [[5sxx\|5sxx]], [[5syh\|5syh]], [[5syi\|5syi]], [[5syj\|5syj]], [[5syk\|5syk]], [[5syl\|5syl]], [[5syu\|5syu]], [[5syv\|5syv]], [[5syw\|5syw]], [[5syx\|5syx]], [[5syy\|5syy]]</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=5sx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sx3 OCA], [http://pdbe.org/5sx3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5sx3 RCSB], [http://www.ebi.ac.uk/pdbsum/5sx3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5sx3 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=5sx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sx3 OCA], [http://pdbe.org/5sx3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5sx3 RCSB], [http://www.ebi.ac.uk/pdbsum/5sx3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5sx3 ProSAT]</span></td></tr>
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	</div>		</div>
	<div class="pdbe-citations 5sx3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5sx3" 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-peroxidase]]		[[Category: Catalase-peroxidase]]

OCA at 14:18, 6 November 2017

2017-11-06T14:18:35Z

←Older revision		Revision as of 14:18, 6 November 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5sx3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5sx3" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Catalase\|Catalase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 09:43, 27 September 2017

2017-09-27T09:43:19Z

←Older revision		Revision as of 09:43, 27 September 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5sx3" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5sx3" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Catalase\|Catalase]]
	== References ==		== References ==
	<references/>		<references/>

OCA: Protected "5sx3" [edit=sysop:move=sysop]

2016-09-09T16:52:42Z

Protected "5sx3" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:52, 9 September 2016

OCA: New page: ==Crystal structure of the catalase-peroxidase KatG of B. pseudomaallei at pH 4.5== == Structural highlights ==
<table><tr><td colspan='2'>[[5sx3]] is a 2 chain structure. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2fxg 2fxg]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SX3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SX3 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5l02|5l02]], [[5l05|5l05]], [[5sw4|5sw4]], [[5sw5|5sw5]], [[5sw6|5sw6]], [[5sx0|5sx0]], [[5sx1|5sx1]], [[5sx2|5sx2]], [[5sx6|5sx6]], [[5sx7|5sx7]], [[5sxq|5sxq]], [[5sxr|5sxr]], [[5sxs|5sxs]], [[5sxt|5sxt]], [[5sxx|5sxx]], [[5syh|5syh]], [[5syi|5syi]], [[5syj|5syj]], [[5syk|5syk]], [[5syl|5syl]], [[5syu|5syu]], [[5syv|5syv]], [[5syw|5syw]], [[5syx|5syx]], [[5syy|5syy]]</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=5sx3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5sx3 OCA], [http://pdbe.org/5sx3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5sx3 RCSB], [http://www.ebi.ac.uk/pdbsum/5sx3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5sx3 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 ==
Crystals of Burkholderia pseudomallei KatG retain their ability to diffract X-rays at high resolution after adjustment of the pH from 5.6 to 4.5, 6.5, 7.5, and 8.5, providing a unique view of the effect of pH on protein structure. One significant pH-sensitive change lies in the appearance of a perhydroxy group attached to the indole nitrogen of the active site Trp111 above pH 7, similar to a modification originally observed in the Ser324Thr variant of the enzyme at pH 5.6. The modification forms rapidly from molecular oxygen in the buffer with 100% occupancy after one minute of soaking of the crystal at room temperature and pH 8.5. The low temperature (4 K) ferric EPR spectra of the resting enzyme, being very sensitive to changes in the heme iron microenvironment, confirm the presence of the modification above pH 7 in native enzyme and variants lacking Arg426 or Met264 and its absence in variants lacking Trp111 or Tyr238. The indole-perhydroxy group is very likely the reactive intermediate of molecular oxygen in the NADH oxidase reaction, and Arg426 is required for its reduction. The second significant pH-sensitive change involves the buried side chain of Arg426 that changes from one predominant conformation at low pH to a second at high pH. The pH profiles of the peroxidase, catalase, and NADH oxidase reactions can be correlated with the distribution of Arg426 conformations. Other pH-induced structural changes include a number of surface-situated side chains, but there is only one change involving a displacement of main chain atoms triggered by the protonation of His53 in a deep pocket in the vicinity of the molecular 2-fold axis.

Roles for Arg426 and Trp111 in the modulation of NADH oxidase activity of the catalase-peroxidase KatG from Burkholderia pseudomallei inferred from pH-induced structural changes.,Carpena X, Wiseman B, Deemagarn T, Herguedas B, Ivancich A, Singh R, Loewen PC, Fita I Biochemistry. 2006 Apr 25;45(16):5171-9. PMID:16618106<ref>PMID:16618106</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5sx3" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Catalase peroxidase]]
[[Category: Loewen, P C]]
[[Category: Catalase-peroxidase]]
[[Category: Katg]]
[[Category: Oxidoreductase]]
[[Category: Ph change]]