1aru - Revision history

OCA at 15:27, 13 March 2024

OCA — Wed, 13 Mar 2024 15:27:38 GMT

←Older revision		Revision as of 15:27, 13 March 2024
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	==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='1aru' size='340' side='right'caption='[[1aru]]' scene=''>	+	<StructureSection load='1aru' size='340' side='right'caption='[[1aru]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ARU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ARU FirstGlance]. <br>
-	</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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [https://pdbe.org/1aru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [https://www.ebi.ac.uk/pdbsum/1aru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1aru ProSAT]</span></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='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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [https://pdbe.org/1aru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [https://www.ebi.ac.uk/pdbsum/1aru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1aru 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]]
Line 18:		Line 22:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Agaricales sp. 'Arthromyces ramosus']]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Amada F]]		[[Category: Amada F]]
	[[Category: Fukuyama K]]		[[Category: Fukuyama K]]
	[[Category: Kunishima N]]		[[Category: Kunishima N]]

OCA at 15:11, 3 March 2021

OCA — Wed, 03 Mar 2021 15:11:37 GMT

←Older revision		Revision as of 15:11, 3 March 2021
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='1aru' size='340' side='right'caption='[[1aru]]~~, [[Resolution\|resolution]] 1.60Å~~' scene=''>	+	<StructureSection load='1aru' size='340' side='right'caption='[[1aru]]' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>~~[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1ARU FirstGlance]. <br>	+	<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ARU 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [https://pdbe.org/1aru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [https://www.ebi.ac.uk/pdbsum/1aru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1aru 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/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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [~~http~~://pdbe.org/1aru PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1aru PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1aru ProSAT]</span></td></tr>	+
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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=1aru 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=1aru 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 1aru" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: 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 09:01, 21 May 2019

OCA — Tue, 21 May 2019 09:01:13 GMT

←Older revision		Revision as of 09:01, 21 May 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='1aru' size='340' side='right' caption='[[1aru]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1aru' size='340' side='right'caption='[[1aru]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARU 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/1aru_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ar/1aru_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 06:18, 17 August 2017

OCA — Thu, 17 Aug 2017 06:18:54 GMT

←Older revision		Revision as of 06:18, 17 August 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='1aru' size='340' side='right' caption='[[1aru]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1aru' size='340' side='right' caption='[[1aru]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARU 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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [http://pdbe.org/1aru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [http://www.ebi.ac.uk/pdbsum/1aru 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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [http://pdbe.org/1aru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [http://www.ebi.ac.uk/pdbsum/1aru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1aru ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		Line 16:
	<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=1aru ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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 00:45, 12 September 2015

OCA — Sat, 12 Sep 2015 00:45:16 GMT

←Older revision		Revision as of 00:45, 12 September 2015
Line 2:		Line 2:
	<StructureSection load='1aru' size='340' side='right' caption='[[1aru]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1aru' size='340' side='right' caption='[[1aru]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARU 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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [http://www.ebi.ac.uk/pdbsum/1aru 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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [http://pdbe.org/1aru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [http://www.ebi.ac.uk/pdbsum/1aru 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 1aru" 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 09:56, 22 December 2014

OCA — Mon, 22 Dec 2014 09:56:43 GMT

←Older revision		Revision as of 09:56, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARU FirstGlance]. <br>		<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARU 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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [http://www.ebi.ac.uk/pdbsum/1aru 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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [http://www.ebi.ac.uk/pdbsum/1aru 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 08:17, 30 July 2014

OCA — Wed, 30 Jul 2014 08:17:42 GMT

←Older revision		Revision as of 08:17, 30 July 2014
Line 1:		Line 1:
-	[[~~Image~~:1aru.~~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='1aru' size='340' side='right' caption='[[1aru]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1aru]] 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=1ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ARU 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=1aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1aru OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1aru RCSB], [http://www.ebi.ac.uk/pdbsum/1aru 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/1aru_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_1aru\| PDB=1aru \| 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__
-	~~[[1aru]] 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=1ARU 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: Protected "1aru" [edit=sysop:move=sysop]

OCA — Sun, 21 Oct 2012 12:26:17 GMT

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

←Older revision

Revision as of 12:26, 21 October 2012

OCA at 12:26, 21 October 2012

OCA — Sun, 21 Oct 2012 12:26:13 GMT

←Older revision		Revision as of 12:26, 21 October 2012
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1aru.png\|left\|200px]]		[[Image:1aru.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1aru", 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_1aru\| PDB=1aru \| SCENE= }}		{{STRUCTURE_1aru\| PDB=1aru \| 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}}

	==About this Structure==		==About this Structure==
-	~~1ARU~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARU OCA].	+	[[1aru]] 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=1ARU OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~7665612~~</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]]
Line 29:		Line 17:
	[[Category: Fukuyama, K.]]		[[Category: Fukuyama, K.]]
	[[Category: Kunishima, N.]]		[[Category: Kunishima, N.]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:30:06 2009''

OCA at 06:30, 18 February 2009

OCA — Wed, 18 Feb 2009 06:30:07 GMT

←Older revision		Revision as of 06:30, 18 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1ARU is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARU OCA].	+	1ARU is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Eukaryota Eukaryota]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ARU OCA].

	==Reference==		==Reference==
-	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:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/7665612 7665612]~~	+	<ref group="xtra">PMID:7665612</ref><references group="xtra"/>
	[[Category: Eukaryota]]		[[Category: Eukaryota]]
	[[Category: Peroxidase]]		[[Category: Peroxidase]]
-	[[Category: Single protein]]
	[[Category: Amada, F.]]		[[Category: Amada, F.]]
	[[Category: Fukuyama, K.]]		[[Category: Fukuyama, K.]]
	[[Category: Kunishima, N.]]		[[Category: Kunishima, N.]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jun 30 17~~:29:~~20 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 08:30:06 2009''