1ccp - Revision history

OCA at 06:42, 7 February 2024

OCA — Wed, 07 Feb 2024 06:42:23 GMT

←Older revision		Revision as of 06:42, 7 February 2024
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	<StructureSection load='1ccp' size='340' side='right'caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1ccp' size='340' side='right'caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_18824 Atcc 18824~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CCP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CCP FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>~~</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]] 2.2Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</div></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	~~<tr~~ id~~='activity'><td class~~="~~sblockLbl~~"><~~b>Activity:</b></td><td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[https://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5]~~ </~~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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [https://pdbe.org/1ccp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [https://www.ebi.ac.uk/pdbsum/1ccp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ccp 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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [https://pdbe.org/1ccp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [https://www.ebi.ac.uk/pdbsum/1ccp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ccp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== 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=1ccp 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=1ccp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	The 2.2-A X-ray structure for CCP(MI), a plasmid-encoded form of Saccharomyces cerevisiae cytochrome c peroxidase (CCP) expressed in Escherichia coli [Fishel, L.A., Villafranca, J. E., Mauro, J. M., & Kraut, J. (1987) Biochemistry 26, 351-360], has been solved, together with the structures of three specifically designed single-site heme-cleft mutants. The structure of CCP(MI) was solved by using molecular replacement methods, since its crystals grow differently from the crystals of CCP isolated from bakers' yeast used previously for structural solution. Small distal-side differences between CCP(MI) and bakers' yeast CCP are observed, presumably due to a strain-specific Thr-53----Ile substitution in CCP(MI). A Trp-51----Phe mutant remains pentacoordinated and exhibits only minor distal structural adjustments. The observation of a vacant sixth coordination site in this structure differs from the results of solution resonance Raman studies, which predict hexacoordinated high-spin iron [Smulevich, G., Mauro, J.M., Fishel, L. A., English, A. M., Kraut, J., & Spiro, T. G. (1988) Biochemistry 27, 5477-5485]. The coordination behavior of this W51F mutant is apparently altered in the presence of a precipitating agent, 30% 2-methyl-2,4-pentanediol. A proximal Trp-191----Phe mutant that has substantially diminished enzyme activity and altered magnetic properties [Mauro, J. M., Fishel, L. F., Hazzard, J. T., Meyer, T. E., Tollin, G., Cusanovich, M. A., & Kraut, J. (1988) Biochemistry 27, 6243-6256] accommodates the substitution by allowing the side chain of Phe-191, together with the segment of backbone to which it is attached, to move toward the heme. This relatively large (ca. 1 A) local perturbation is accompanied by numerous small adjustments resulting in a slight overall compression of the enzyme's proximal domain; however, the iron coordination sphere is essentially unchanged. This structure rules out a major alteration in protein conformation as a reason for the dramatically decreased activity of the W191F mutant. Changing proximal Asp-235 to Asn results in two significant localized structural changes. First, the heme iron moves toward the porphyrin plane, and distal water 595 now clearly resides in the iron coordination sphere at a distance of 2.0 A. The observation of hexacoordinated iron for the D235N mutant is in accord with previous resonance Raman results. Second, the indole side chain of Trp-191 has flipped over as a result of the mutation; the tryptophan N epsilon takes part in a new hydrogen bond with the backbone carbonyl oxygen of Leu-177.(ABSTRACT TRUNCATED AT 400 WORDS)
-
-	X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis.,Wang JM, Mauro M, Edwards SL, Oatley SJ, Fishel LA, Ashford VA, Xuong NH, Kraut J Biochemistry. 1990 Aug 7;29(31):7160-73. PMID:2169873<ref>PMID:2169873</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1ccp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]		*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
-	[[Category: Cytochrome-c peroxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ashford~~, V A~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Edwards~~, S L~~]]	+	[[Category: Ashford VA]]
-	[[Category: Fishel~~, L A~~]]	+	[[Category: Edwards SL]]
-	[[Category: Kraut, J]]	+	[[Category: Fishel LA]]
-	[[Category: Mauro~~, J M~~]]	+	[[Category: Kraut J]]
-	[[Category: Oatley~~, S J~~]]	+	[[Category: Mauro JM]]
-	[[Category: Wang, J]]	+	[[Category: Oatley SJ]]
-	[[Category: Xuong, N H]]	+	[[Category: Wang J]]
-	~~[[Category: Oxidoreductase~~]]	+	[[Category: Xuong N-H]]

OCA at 10:35, 14 July 2021

OCA — Wed, 14 Jul 2021 10:35:33 GMT

←Older revision		Revision as of 10:35, 14 July 2021
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	<StructureSection load='1ccp' size='340' side='right'caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1ccp' size='340' side='right'caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1CCP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CCP FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [~~http~~://pdbe.org/1ccp PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1ccp PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1ccp 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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [https://pdbe.org/1ccp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [https://www.ebi.ac.uk/pdbsum/1ccp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ccp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.	+	[[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 07:31, 10 October 2019

OCA — Thu, 10 Oct 2019 07:31:05 GMT

←Older revision		Revision as of 07:31, 10 October 2019
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	==X-RAY STRUCTURES OF RECOMBINANT YEAST CYTOCHROME C PEROXIDASE AND THREE HEME-CLEFT MUTANTS PREPARED BY SITE-DIRECTED MUTAGENESIS==		==X-RAY STRUCTURES OF RECOMBINANT YEAST CYTOCHROME C PEROXIDASE AND THREE HEME-CLEFT MUTANTS PREPARED BY SITE-DIRECTED MUTAGENESIS==
-	<StructureSection load='1ccp' size='340' side='right' caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>	+	<StructureSection load='1ccp' size='340' side='right'caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CCP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CCP FirstGlance]. <br>
Line 15:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cc/1ccp_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cc/1ccp_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 30:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1ccp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ccp" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
Line 36:		Line 39:
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
		+	[[Category: Large Structures]]
	[[Category: Ashford, V A]]		[[Category: Ashford, V A]]
	[[Category: Edwards, S L]]		[[Category: Edwards, S L]]

OCA at 06:27, 29 November 2017

OCA — Wed, 29 Nov 2017 06:27:56 GMT

←Older revision		Revision as of 06:27, 29 November 2017
Line 1:		Line 1:
		+
	==X-RAY STRUCTURES OF RECOMBINANT YEAST CYTOCHROME C PEROXIDASE AND THREE HEME-CLEFT MUTANTS PREPARED BY SITE-DIRECTED MUTAGENESIS==		==X-RAY STRUCTURES OF RECOMBINANT YEAST CYTOCHROME C PEROXIDASE AND THREE HEME-CLEFT MUTANTS PREPARED BY SITE-DIRECTED MUTAGENESIS==
	<StructureSection load='1ccp' size='340' side='right' caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1ccp' size='340' side='right' caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [http://pdbe.org/1ccp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [http://www.ebi.ac.uk/pdbsum/1ccp 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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [http://pdbe.org/1ccp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [http://www.ebi.ac.uk/pdbsum/1ccp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ccp ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1ccp" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1ccp" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 02:01, 9 February 2016

OCA — Tue, 09 Feb 2016 02:01:07 GMT

←Older revision		Revision as of 02:01, 9 February 2016
Line 18:		Line 18:
	<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=1ccp ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 17:31, 10 September 2015

OCA — Thu, 10 Sep 2015 17:31:21 GMT

←Older revision		Revision as of 17:31, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1ccp' size='340' side='right' caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1ccp' size='340' side='right' caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Saccharomyces_cerevisiae Saccharomyces cerevisiae~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CCP FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CCP FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [http://www.ebi.ac.uk/pdbsum/1ccp 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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [http://pdbe.org/1ccp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [http://www.ebi.ac.uk/pdbsum/1ccp PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	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 1ccp" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 35:		Line 36:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Ashford, V A]]		[[Category: Ashford, V A]]
	[[Category: Edwards, S L]]		[[Category: Edwards, S L]]

OCA at 03:39, 25 December 2014

OCA — Thu, 25 Dec 2014 03:39:17 GMT

←Older revision		Revision as of 03:39, 25 December 2014
Line 8:		Line 8:
	<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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [http://www.ebi.ac.uk/pdbsum/1ccp 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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [http://www.ebi.ac.uk/pdbsum/1ccp PDBsum]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 10:26, 22 December 2014

OCA — Mon, 22 Dec 2014 10:26:26 GMT

←Older revision		Revision as of 10:26, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CCP FirstGlance]. <br>		<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CCP FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [http://www.ebi.ac.uk/pdbsum/1ccp 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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [http://www.ebi.ac.uk/pdbsum/1ccp 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 35:		Line 35:
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Ashford, V A.]]	+	[[Category: Ashford, V A]]
-	[[Category: Edwards, S L.]]	+	[[Category: Edwards, S L]]
-	[[Category: Fishel, L A.]]	+	[[Category: Fishel, L A]]
-	[[Category: Kraut, J.]]	+	[[Category: Kraut, J]]
-	[[Category: Mauro, J M.]]	+	[[Category: Mauro, J M]]
-	[[Category: Oatley, S J.]]	+	[[Category: Oatley, S J]]
-	[[Category: Wang, J.]]	+	[[Category: Wang, J]]
-	[[Category: Xuong, N H.]]	+	[[Category: Xuong, N H]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 17:14, 20 August 2014

OCA — Wed, 20 Aug 2014 17:14:46 GMT

←Older revision		Revision as of 17:14, 20 August 2014
Line 1:		Line 1:
-	[[~~Image:~~1ccp.~~png~~\|~~left~~\|200px]]	+	==X-RAY STRUCTURES OF RECOMBINANT YEAST CYTOCHROME C PEROXIDASE AND THREE HEME-CLEFT MUTANTS PREPARED BY SITE-DIRECTED MUTAGENESIS==
		+	<StructureSection load='1ccp' size='340' side='right' caption='[[1ccp]], [[Resolution\|resolution]] 2.20Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1ccp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1CCP FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2ccp\|2ccp]], [[3ccp\|3ccp]], [[4ccp\|4ccp]], [[5ccp\|5ccp]], [[6ccp\|6ccp]], [[7ccp\|7ccp]], [[1cpd\|1cpd]], [[1cpe\|1cpe]], [[1cpf\|1cpf]], [[1cpg\|1cpg]], [[1bej\|1bej]], [[1bem\|1bem]], [[1beq\|1beq]], [[1bes\|1bes]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </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=1ccp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ccp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ccp RCSB], [http://www.ebi.ac.uk/pdbsum/1ccp 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/cc/1ccp_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 2.2-A X-ray structure for CCP(MI), a plasmid-encoded form of Saccharomyces cerevisiae cytochrome c peroxidase (CCP) expressed in Escherichia coli [Fishel, L.A., Villafranca, J. E., Mauro, J. M., & Kraut, J. (1987) Biochemistry 26, 351-360], has been solved, together with the structures of three specifically designed single-site heme-cleft mutants. The structure of CCP(MI) was solved by using molecular replacement methods, since its crystals grow differently from the crystals of CCP isolated from bakers' yeast used previously for structural solution. Small distal-side differences between CCP(MI) and bakers' yeast CCP are observed, presumably due to a strain-specific Thr-53----Ile substitution in CCP(MI). A Trp-51----Phe mutant remains pentacoordinated and exhibits only minor distal structural adjustments. The observation of a vacant sixth coordination site in this structure differs from the results of solution resonance Raman studies, which predict hexacoordinated high-spin iron [Smulevich, G., Mauro, J.M., Fishel, L. A., English, A. M., Kraut, J., & Spiro, T. G. (1988) Biochemistry 27, 5477-5485]. The coordination behavior of this W51F mutant is apparently altered in the presence of a precipitating agent, 30% 2-methyl-2,4-pentanediol. A proximal Trp-191----Phe mutant that has substantially diminished enzyme activity and altered magnetic properties [Mauro, J. M., Fishel, L. F., Hazzard, J. T., Meyer, T. E., Tollin, G., Cusanovich, M. A., & Kraut, J. (1988) Biochemistry 27, 6243-6256] accommodates the substitution by allowing the side chain of Phe-191, together with the segment of backbone to which it is attached, to move toward the heme. This relatively large (ca. 1 A) local perturbation is accompanied by numerous small adjustments resulting in a slight overall compression of the enzyme's proximal domain; however, the iron coordination sphere is essentially unchanged. This structure rules out a major alteration in protein conformation as a reason for the dramatically decreased activity of the W191F mutant. Changing proximal Asp-235 to Asn results in two significant localized structural changes. First, the heme iron moves toward the porphyrin plane, and distal water 595 now clearly resides in the iron coordination sphere at a distance of 2.0 A. The observation of hexacoordinated iron for the D235N mutant is in accord with previous resonance Raman results. Second, the indole side chain of Trp-191 has flipped over as a result of the mutation; the tryptophan N epsilon takes part in a new hydrogen bond with the backbone carbonyl oxygen of Leu-177.(ABSTRACT TRUNCATED AT 400 WORDS)

-	~~{{STRUCTURE_1ccp\| PDB=1ccp \| SCENE= }}~~	+	X-ray structures of recombinant yeast cytochrome c peroxidase and three heme-cleft mutants prepared by site-directed mutagenesis.,Wang JM, Mauro M, Edwards SL, Oatley SJ, Fishel LA, Ashford VA, Xuong NH, Kraut J Biochemistry. 1990 Aug 7;29(31):7160-73. PMID:2169873<ref>PMID:2169873</ref>

-	~~===X-RAY STRUCTURES OF RECOMBINANT YEAST CYTOCHROME C PEROXIDASE AND THREE HEME-CLEFT MUTANTS PREPARED BY SITE-DIRECTED MUTAGENESIS===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_2169873}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1ccp]] is~~ a ~~1 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA].~~	+

	==See Also==		==See Also==
	*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]		*[[Cytochrome c peroxidase\|Cytochrome c peroxidase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:002169873<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

OCA at 12:15, 20 October 2012

OCA — Sat, 20 Oct 2012 12:15:50 GMT

←Older revision		Revision as of 12:15, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1ccp]] is a 1 chain structure ~~of [[Cytochrome c peroxidase]]~~ with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA].	+	[[1ccp]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CCP OCA].

	==See Also==		==See Also==