5syi - Revision history

OCA at 12:50, 4 October 2023

OCA — Wed, 04 Oct 2023 12:50:58 GMT

←Older revision		Revision as of 12:50, 4 October 2023
Line 3:		Line 3:
	<StructureSection load='5syi' size='340' side='right'caption='[[5syi]], [[Resolution\|resolution]] 1.70Å' scene=''>		<StructureSection load='5syi' size='340' side='right'caption='[[5syi]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5syi]] 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=4ka6 4ka6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SYI OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5SYI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5syi]] 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=4ka6 4ka6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5SYI 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=NIZ:PYRIDINE-4-CARBOHYDRAZIDE'>NIZ</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 1.7Å</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]], [[5sx3\|5sx3]], [[5sx6\|5sx6]], [[5sx7\|5sx7]], [[5sxq\|5sxq]], [[5sxr\|5sxr]], [[5sxs\|5sxs]], [[5sxt\|5sxt]], [[5sxx\|5sxx]], [[5syh\|5syh]], [[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=NIZ:PYRIDINE-4-CARBOHYDRAZIDE'>NIZ</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=5syi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5syi OCA], [https://pdbe.org/5syi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5syi RCSB], [https://www.ebi.ac.uk/pdbsum/5syi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5syi 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=5syi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5syi OCA], [~~http~~://pdbe.org/5syi PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5syi RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5syi PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5syi 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: D141a variant]]~~	+
-	~~[[Category: Isoniazid]]~~	+
-	~~[[Category: Katg]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 08:14, 8 January 2020

OCA — Wed, 08 Jan 2020 08:14:42 GMT

←Older revision		Revision as of 08:14, 8 January 2020
Line 1:		Line 1:

	==Structure of D141A variant of B. pseudomallei KatG complexed with INH==		==Structure of D141A variant of B. pseudomallei KatG complexed with INH==
-	<StructureSection load='5syi' size='340' side='right' caption='[[5syi]], [[Resolution\|resolution]] 1.70Å' scene=''>	+	<StructureSection load='5syi' size='340' side='right'caption='[[5syi]], [[Resolution\|resolution]] 1.70Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5syi]] 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=4ka6 4ka6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SYI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SYI FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5syi]] 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=4ka6 4ka6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SYI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SYI 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=NIZ:PYRIDINE-4-CARBOHYDRAZIDE'>NIZ</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"><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=NIZ:PYRIDINE-4-CARBOHYDRAZIDE'>NIZ</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]], [[5sx3\|5sx3]], [[5sx6\|5sx6]], [[5sx7\|5sx7]], [[5sxq\|5sxq]], [[5sxr\|5sxr]], [[5sxs\|5sxs]], [[5sxt\|5sxt]], [[5sxx\|5sxx]], [[5syh\|5syh]], [[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]], [[5sx3\|5sx3]], [[5sx6\|5sx6]], [[5sx7\|5sx7]], [[5sxq\|5sxq]], [[5sxr\|5sxr]], [[5sxs\|5sxs]], [[5sxt\|5sxt]], [[5sxx\|5sxx]], [[5syh\|5syh]], [[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=5syi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5syi OCA], [http://pdbe.org/5syi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5syi RCSB], [http://www.ebi.ac.uk/pdbsum/5syi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5syi 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=5syi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5syi OCA], [http://pdbe.org/5syi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5syi RCSB], [http://www.ebi.ac.uk/pdbsum/5syi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5syi ProSAT]</span></td></tr>
Line 20:		Line 21:
	</div>		</div>
	<div class="pdbe-citations 5syi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5syi" 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

OCA — Mon, 06 Nov 2017 14:18:56 GMT

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

OCA at 10:09, 27 September 2017

OCA — Wed, 27 Sep 2017 10:09:35 GMT

←Older revision		Revision as of 10:09, 27 September 2017
Line 20:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 5syi" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5syi" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Catalase\|Catalase]]
	== References ==		== References ==
	<references/>		<references/>

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

OCA — Fri, 09 Sep 2016 16:53:22 GMT

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

←Older revision

Revision as of 16:53, 9 September 2016

OCA: New page: ==Structure of D141A variant of B. pseudomallei KatG complexed with INH==
OCA — Fri, 09 Sep 2016 16:53:19 GMT

New page: ==Structure of D141A variant of B. pseudomallei KatG complexed with INH== <StructureSection load='5syi' size='340' side='right' caption='5syi, resolution 1.70Å' s...

New page

==Structure of D141A variant of B. pseudomallei KatG complexed with INH==
<StructureSection load='5syi' size='340' side='right' caption='[[5syi]], [[Resolution|resolution]] 1.70Å' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5syi]] 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=4ka6 4ka6]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5SYI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5SYI 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=NIZ:PYRIDINE-4-CARBOHYDRAZIDE'>NIZ</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]], [[5sx3|5sx3]], [[5sx6|5sx6]], [[5sx7|5sx7]], [[5sxq|5sxq]], [[5sxr|5sxr]], [[5sxs|5sxs]], [[5sxt|5sxt]], [[5sxx|5sxx]], [[5syh|5syh]], [[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=5syi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5syi OCA], [http://pdbe.org/5syi PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5syi RCSB], [http://www.ebi.ac.uk/pdbsum/5syi PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5syi 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 ==
Isonicotinic acid hydrazide (isoniazid or INH) is a front line antitubercular pro-drug that is converted to its active form, isonicotinyl-NAD, by the bacterial catalase-peroxidase KatG. Understanding the role of KatG in the INH activation process has been hampered by a lack of knowledge of the actual drug binding site. In this work, we have investigated the binding of INH in the main access channel of KatG with a combination of molecular dynamics, using an enhanced-sampling technique (metadynamics), X-ray crystallography, and site-directed mutagenesis. The metadynamics simulations show that there are several weak drug binding sites along the access channel. Moreover, the simulations evidence that complete entrance to the heme active site is impeded by an aspartate residue (D141) located above the heme. This has been confirmed by structural and functional analysis of the D141A mutant, leading to the first X-ray crystallography evidence of INH at the heme access channel.

Binding of the Antitubercular Pro-Drug Isoniazid in the Heme Access Channel of Catalase-Peroxidase (KatG). A Combined Structural and Metadynamics Investigation.,Vidossich P, Loewen PC, Carpena X, Fiorin G, Fita I, Rovira C J Phys Chem B. 2014 Mar 20;118(11):2924-31. doi: 10.1021/jp4123425. Epub 2014 Mar, 7. PMID:24568093<ref>PMID:24568093</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 5syi" style="background-color:#fffaf0;"></div>
== References ==
<references/>
TOC
</StructureSection>
[[Category: Catalase peroxidase]]
[[Category: Loewen, P C]]
[[Category: Catalase-peroxidase]]
[[Category: D141a variant]]
[[Category: Isoniazid]]
[[Category: Katg]]
[[Category: Oxidoreductase]]