6p42 - Revision history

OCA at 07:22, 11 October 2023

2023-10-11T07:22:49Z

←Older revision		Revision as of 07:22, 11 October 2023
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	<StructureSection load='6p42' size='340' side='right'caption='[[6p42]], [[Resolution\|resolution]] 2.91Å' scene=''>		<StructureSection load='6p42' size='340' side='right'caption='[[6p42]], [[Resolution\|resolution]] 2.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p42]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Baker's_yeast Baker's yeast~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P42 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6P42 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p42]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P42 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6P42 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='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.905Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">CCP1, CCP, CPO, YKR066C ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=559292 Baker's yeast]), CYC1, YJR048W, J1653 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])~~</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~~'>~~[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'>[https://proteopedia.org/fgij/fg.htm?mol=6p42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p42 OCA], [https://pdbe.org/6p42 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6p42 RCSB], [https://www.ebi.ac.uk/pdbsum/6p42 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6p42 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6p42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p42 OCA], [~~http~~://pdbe.org/6p42 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6p42 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6p42 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6p42 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. [[http://www.uniprot.org/uniprot/CYC1_YEAST CYC1_YEAST]] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.	+	[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.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</div>		</div>
	<div class="pdbe-citations 6p42" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6p42" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Cytochrome C 3D structures\|Cytochrome C 3D structures]]
		+	*[[Cytochrome c peroxidase 3D structures\|Cytochrome c peroxidase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Baker's yeast]]
-	[[Category: Cytochrome-c peroxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Crane, B R~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Yee, E F~~]]	+	[[Category: Crane BR]]
-	[[Category: ~~Electron hopping]]~~	+	[[Category: Yee EF]]
-	~~[[Category: Electron transport]]~~	+
-	~~[[Category: Electron transport-oxidoreductase complex]]~~	+
-	~~[[Category: Heme protein]]~~	+
-	~~[[Category: Multi-step tunneling~~]]	+

OCA at 17:47, 20 November 2019

2019-11-20T17:47:28Z

←Older revision		Revision as of 17:47, 20 November 2019
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	<StructureSection load='6p42' size='340' side='right'caption='[[6p42]], [[Resolution\|resolution]] 2.91Å' scene=''>		<StructureSection load='6p42' size='340' side='right'caption='[[6p42]], [[Resolution\|resolution]] 2.91Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6p42]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P42 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6p42]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P42 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='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CCP1, CCP, CPO, YKR066C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast]), CYC1, YJR048W, J1653 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=6p42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p42 OCA], [http://pdbe.org/6p42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p42 RCSB], [http://www.ebi.ac.uk/pdbsum/6p42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p42 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6p42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p42 OCA], [http://pdbe.org/6p42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p42 RCSB], [http://www.ebi.ac.uk/pdbsum/6p42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p42 ProSAT]</span></td></tr>
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Baker's yeast]]
	[[Category: Cytochrome-c peroxidase]]		[[Category: Cytochrome-c peroxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:56, 23 October 2019

2019-10-23T06:56:47Z

←Older revision		Revision as of 06:56, 23 October 2019
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-	'''Unreleased structure'''

-	~~The entry~~ 6p42 is ~~ON HOLD until Paper~~ Publication	+	==Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c==
		+	<StructureSection load='6p42' size='340' side='right'caption='[[6p42]], [[Resolution\|resolution]] 2.91Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6p42]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6P42 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6P42 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>
		+	<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=6p42 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6p42 OCA], [http://pdbe.org/6p42 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6p42 RCSB], [http://www.ebi.ac.uk/pdbsum/6p42 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6p42 ProSAT]</span></td></tr>
		+	</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. [[http://www.uniprot.org/uniprot/CYC1_YEAST CYC1_YEAST]] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transient tyrosine and tryptophan radicals play key roles in the electron transfer (ET) reactions of photosystem (PS) II, ribonucleotide reductase (RNR), photolyase and many other proteins. However, Tyr and Trp are not functionally interchangeable and the factors controlling their reactivity are often unclear. Cytochrome c peroxidase (CcP) employs a Trp191(+) radical to oxidize reduced cytochrome c (Cc). Although a Tyr191 replacement also forms a stable radical, it does not support rapid ET from Cc. Here we probe the redox properties of CcP Y191 by non-natural amino acid substitution, altering the ET driving force, and manipulating the protic environment of Y191. Higher potential fluorotyrosine residues increase ET rates marginally, but only addition of a hydrogen bond donor to Tyr191() (via Leu232His or Glu) rescues activity by increasing the ET rate by nearly 30-fold. ESR and ESEEM spectroscopies, crystallography, and pH-dependent ET kinetics provide strong evidence for hydrogen bond formation to Y191() by His232/Glu232. Rate measurements and rapid freeze quench ESR spectroscopy further reveal differences in radical propagation and Cc oxidation that support an increased Y191() reduction potential of approximately 200 mV in the presence of E232. Hence, Y191 inactivity results from a reduction potential drop owing to Y191(+) deprotonation. Incorporation of a well-positioned base to accept and donate back a hydrogen bond upshifts the Tyr() potential into a range where it can effectively oxidize Cc. These findings have implications for the YZ/YD radicals of PS II, hole-hopping in RNR and cryptochrome, and engineering proteins for long-range ET reactions.

-	~~Authors: Yee, E.F~~., ~~Crane~~, B.R.	+	Tuning radical relay residues by proton management rescues protein electron hopping.,Yee EF, Dzikovski B, Crane BR J Am Chem Soc. 2019 Oct 11. doi: 10.1021/jacs.9b05715. PMID:31603693<ref>PMID:31603693</ref>

-	~~Description~~: ~~Yeast cytochrome c peroxidase (W191Y~~:~~L232H) in complex with iso~~-~~1 cytochrome~~ c	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: Yee, E.F]]	+	<div class="pdbe-citations 6p42" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Crane, B.R~~]]	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Cytochrome-c peroxidase]]
		+	[[Category: Large Structures]]
		+	[[Category: Crane, B R]]
		+	[[Category: Yee, E F]]
		+	[[Category: Electron hopping]]
		+	[[Category: Electron transport]]
		+	[[Category: Electron transport-oxidoreductase complex]]
		+	[[Category: Heme protein]]
		+	[[Category: Multi-step tunneling]]

OCA at 04:10, 3 July 2019

2019-07-03T04:10:51Z

←Older revision		Revision as of 04:10, 3 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6p42 is ON HOLD	+	The entry 6p42 is ON HOLD until Paper Publication

	Authors: Yee, E.F., Crane, B.R.		Authors: Yee, E.F., Crane, B.R.
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	Description: Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c		Description: Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Crane, B.R]]
	[[Category: Yee, E.F]]		[[Category: Yee, E.F]]
		+	[[Category: Crane, B.R]]

OCA: Protected "6p42" [edit=sysop:move=sysop]

2019-06-05T21:12:08Z

Protected "6p42" [edit=sysop:move=sysop]

←Older revision

Revision as of 21:12, 5 June 2019

OCA: New page: '''Unreleased structure''' The entry 6p42 is ON HOLD Authors: Yee, E.F., Crane, B.R. Description: Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c [[Categ...

2019-06-05T21:12:06Z

New page: '''Unreleased structure''' The entry 6p42 is ON HOLD Authors: Yee, E.F., Crane, B.R. Description: Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c [[Categ...

New page

'''Unreleased structure'''

The entry 6p42 is ON HOLD

Authors: Yee, E.F., Crane, B.R.

Description: Yeast cytochrome c peroxidase (W191Y:L232H) in complex with iso-1 cytochrome c
[[Category: Unreleased Structures]]
[[Category: Crane, B.R]]
[[Category: Yee, E.F]]