1arv - Revision history

OCA at 15:27, 13 March 2024

OCA — Wed, 13 Mar 2024 15:27:39 GMT

←Older revision		Revision as of 15:27, 13 March 2024
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	<StructureSection load='1arv' size='340' side='right'caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1arv' size='340' side='right'caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/'~~arthromyces_ramosus~~' '~~arthromyces~~ ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ARV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Agaricales_sp._'Arthromyces_ramosus' Agaricales sp. 'Arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ARV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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]] 1.6Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [https://pdbe.org/1arv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [https://www.ebi.ac.uk/pdbsum/1arv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1arv 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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [https://pdbe.org/1arv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [https://www.ebi.ac.uk/pdbsum/1arv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1arv ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PER_ARTRA PER_ARTRA]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</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=1arv ConSurf].		</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=1arv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The structures of the cyanide and triiodide complexes of Arthromyces ramosus peroxidase (ARP) at different pH values were investigated by x-ray crystallography in order to examine the behavior of the invariant residues of arginine (Arg-52) and distal histidine (His-56) during the enzyme reaction as well as to provide the structural basis of the active site of peroxidase. The models of the cyanide complexes at pH 7.5, 5.0, and 4.0, respectively, were refined to the R-factors of 17.8, 17.8, and 18.5% using 7.0-1.6-A resolution data, and those of the triiodide complexes at pH 6.5 and 5.0 refined to 16.9 and 16.8% using 7.0-1.9-A resolution data. The structures of the cyanide complexes at pH 7.5, 5.0, and 4.0 are identical within experimental error. Cyanide ion bound to the heme in the bent conformation rather than in the tilt conformation. Upon cyanide ion binding, the N epsilon atom of His-56 moved toward the ion by rotation of the imidazole ring around the C beta-C gamma bond, but there was little conformational change in the remaining residues. The distance between the N epsilon atom of His-56 and the nitrogen atom of the cyanide suggests the presence of a hydrogen bond between them in the pH range investigated. In the triiodide complexes, one of the two triiodides bound to ARP was located at the distal side of the heme. When triiodide bound to ARP, unlike the rearrangement of the distal arginine of cytochrome c peroxidase that occurs on formation of the fluoride complex or compound I, the side chain of Arg-52 moved little. The conformation of the side chain of His-56, however, changed markedly. Conformational flexibility of His-56 appears to be a requisite for proton translocation from one oxygen atom to the other of HOO- by acid-base catalysis to produce compound I. The iron atom in each cyanide complex (low-spin ferric) is located in the heme plane, whereas in each triiodide complex (high-spin ferric) the iron atom is displaced from the plane about 0.2 A toward the proximal side.
-
-	Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis.,Fukuyama K, Kunishima N, Amada F, Kubota T, Matsubara H J Biol Chem. 1995 Sep 15;270(37):21884-92. PMID:7665612<ref>PMID:7665612</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1arv" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Arthromyces ramosus]]	+	[[Category: Agaricales sp. 'Arthromyces ramosus']]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Peroxidase]]~~	+	[[Category: Amada F]]
-	[[Category: Amada, F]]	+	[[Category: Fukuyama K]]
-	[[Category: Fukuyama, K]]	+	[[Category: Kunishima N]]
-	[[Category: Kunishima, N]]	+

OCA at 09:48, 26 May 2021

OCA — Wed, 26 May 2021 09:48:10 GMT

←Older revision		Revision as of 09:48, 26 May 2021
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	<StructureSection load='1arv' size='340' side='right'caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1arv' size='340' side='right'caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ARV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ARV FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [~~http~~://pdbe.org/1arv PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1arv PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1arv 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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [https://pdbe.org/1arv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [https://www.ebi.ac.uk/pdbsum/1arv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1arv ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 07:30, 21 August 2019

OCA — Wed, 21 Aug 2019 07:30:46 GMT

←Older revision		Revision as of 07:30, 21 August 2019
Line 1:		Line 1:

	==CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS==		==CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS==
-	<StructureSection load='1arv' size='340' side='right' caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1arv' size='340' side='right'caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARV FirstGlance]. <br>
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ar/1arv_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ar/1arv_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Arthromyces ramosus]]		[[Category: Arthromyces ramosus]]
		+	[[Category: Large Structures]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
	[[Category: Amada, F]]		[[Category: Amada, F]]
	[[Category: Fukuyama, K]]		[[Category: Fukuyama, K]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]

OCA at 10:32, 15 November 2017

OCA — Wed, 15 Nov 2017 10:32:50 GMT

←Older revision		Revision as of 10:32, 15 November 2017
Line 1:		Line 1:
		+
	==CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS==		==CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS==
	<StructureSection load='1arv' size='340' side='right' caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1arv' size='340' side='right' caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Agaricales_sp._~~'arthromyces_ramosus' ~~Agaricales sp.~~ 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/'arthromyces_ramosus' 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [http://pdbe.org/1arv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [http://www.ebi.ac.uk/pdbsum/1arv 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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [http://pdbe.org/1arv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [http://www.ebi.ac.uk/pdbsum/1arv PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1arv ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Agaricales sp. 'arthromyces~~ ramosus']]	+	[[Category: Arthromyces ramosus]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
	[[Category: Amada, F]]		[[Category: Amada, F]]
	[[Category: Fukuyama, K]]		[[Category: Fukuyama, K]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]

OCA at 04:55, 10 February 2016

OCA — Wed, 10 Feb 2016 04:55:20 GMT

←Older revision		Revision as of 04:55, 10 February 2016
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=1arv ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:35, 11 September 2015

OCA — Fri, 11 Sep 2015 05:35:08 GMT

←Older revision		Revision as of 05:35, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1arv' size='340' side='right' caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1arv' size='340' side='right' caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Eukaryota Eukaryota~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARV FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Agaricales_sp._'arthromyces_ramosus' Agaricales sp. 'arthromyces ramosus']. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARV FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [http://www.ebi.ac.uk/pdbsum/1arv 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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [http://pdbe.org/1arv PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [http://www.ebi.ac.uk/pdbsum/1arv PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	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 1arv" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Eukaryota~~]]	+	[[Category: Agaricales sp. 'arthromyces ramosus']]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
	[[Category: Amada, F]]		[[Category: Amada, F]]
	[[Category: Fukuyama, K]]		[[Category: Fukuyama, K]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]

OCA at 09:59, 22 December 2014

OCA — Mon, 22 Dec 2014 09:59:11 GMT

←Older revision		Revision as of 09:59, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARV FirstGlance]. <br>		<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARV FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [http://www.ebi.ac.uk/pdbsum/1arv 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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [http://www.ebi.ac.uk/pdbsum/1arv PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 31:		Line 31:
	[[Category: Eukaryota]]		[[Category: Eukaryota]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
-	[[Category: Amada, F.]]	+	[[Category: Amada, F]]
-	[[Category: Fukuyama, K.]]	+	[[Category: Fukuyama, K]]
-	[[Category: Kunishima, N.]]	+	[[Category: Kunishima, N]]

OCA at 08:05, 30 July 2014

OCA — Wed, 30 Jul 2014 08:05:33 GMT

←Older revision		Revision as of 08:05, 30 July 2014
Line 1:		Line 1:
-	[[~~Image~~:1arv.~~png\|left~~\|200px]]	+	==CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS==
		+	<StructureSection load='1arv' size='340' side='right' caption='[[1arv]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1arv]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARV FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CYN:CYANIDE+ION'>CYN</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Peroxidase Peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.7 1.11.1.7] </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=1arv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1arv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1arv RCSB], [http://www.ebi.ac.uk/pdbsum/1arv PDBsum]</span></td></tr>
		+	<table>
		+	== 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/ar/1arv_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/chain_selection.php?pdb_ID=2ata ConSurf].
		+	<div style="clear:both"></div>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The structures of the cyanide and triiodide complexes of Arthromyces ramosus peroxidase (ARP) at different pH values were investigated by x-ray crystallography in order to examine the behavior of the invariant residues of arginine (Arg-52) and distal histidine (His-56) during the enzyme reaction as well as to provide the structural basis of the active site of peroxidase. The models of the cyanide complexes at pH 7.5, 5.0, and 4.0, respectively, were refined to the R-factors of 17.8, 17.8, and 18.5% using 7.0-1.6-A resolution data, and those of the triiodide complexes at pH 6.5 and 5.0 refined to 16.9 and 16.8% using 7.0-1.9-A resolution data. The structures of the cyanide complexes at pH 7.5, 5.0, and 4.0 are identical within experimental error. Cyanide ion bound to the heme in the bent conformation rather than in the tilt conformation. Upon cyanide ion binding, the N epsilon atom of His-56 moved toward the ion by rotation of the imidazole ring around the C beta-C gamma bond, but there was little conformational change in the remaining residues. The distance between the N epsilon atom of His-56 and the nitrogen atom of the cyanide suggests the presence of a hydrogen bond between them in the pH range investigated. In the triiodide complexes, one of the two triiodides bound to ARP was located at the distal side of the heme. When triiodide bound to ARP, unlike the rearrangement of the distal arginine of cytochrome c peroxidase that occurs on formation of the fluoride complex or compound I, the side chain of Arg-52 moved little. The conformation of the side chain of His-56, however, changed markedly. Conformational flexibility of His-56 appears to be a requisite for proton translocation from one oxygen atom to the other of HOO- by acid-base catalysis to produce compound I. The iron atom in each cyanide complex (low-spin ferric) is located in the heme plane, whereas in each triiodide complex (high-spin ferric) the iron atom is displaced from the plane about 0.2 A toward the proximal side.

-	~~{{STRUCTURE_1arv\| PDB=1arv \| SCENE= }}~~	+	Crystal structures of cyanide- and triiodide-bound forms of Arthromyces ramosus peroxidase at different pH values. Perturbations of active site residues and their implication in enzyme catalysis.,Fukuyama K, Kunishima N, Amada F, Kubota T, Matsubara H J Biol Chem. 1995 Sep 15;270(37):21884-92. PMID:7665612<ref>PMID:7665612</ref>

-	~~===CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_7665612}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1arv]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Eukaryota Eukaryota]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1ARV OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:007665612<~~/~~ref~~><~~ref group="xtra">PMID:011604529</ref><references group="xtra"~~/>	+
	[[Category: Eukaryota]]		[[Category: Eukaryota]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]

OCA at 14:22, 21 October 2012

OCA — Sun, 21 Oct 2012 14:22:55 GMT

←Older revision		Revision as of 14:22, 21 October 2012
Line 1:		Line 1:
	[[Image:1arv.png\|left\|200px]]		[[Image:1arv.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1arv", 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_1arv\| PDB=1arv \| SCENE= }}		{{STRUCTURE_1arv\| PDB=1arv \| SCENE= }}

	===CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS===		===CRYSTAL STRUCTURES OF CYANIDE-AND TRIIODIDE-BOUND FORMS OF ARTHROMYCES RAMOSUS PEROXIDASE AT DIFFERENT PH VALUES. PERTURBATIONS OF ACTIVE SITE RESIDUES AND THEIR IMPLICATION IN ENZYME CATALYSIS===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_7665612}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 7665612 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_7665612}}		{{ABSTRACT_PUBMED_7665612}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:007665612</ref><ref group="xtra">PMID:011604529~~</ref><ref group="xtra">PMID:011917145</ref><ref group="xtra">PMID:012777760~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:007665612</ref><ref group="xtra">PMID:011604529</ref><references group="xtra"/>
	[[Category: Eukaryota]]		[[Category: Eukaryota]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]

OCA: Protected "1arv" [edit=sysop:move=sysop]

OCA — Thu, 28 Apr 2011 12:52:21 GMT

Protected "1arv" [edit=sysop:move=sysop]

←Older revision

Revision as of 12:52, 28 April 2011