1tkl - Revision history

OCA at 08:40, 14 February 2024

2024-02-14T08:40:13Z

←Older revision		Revision as of 08:40, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1tkl' size='340' side='right'caption='[[1tkl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1tkl' size='340' side='right'caption='[[1tkl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tkl]] is a 2 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=1TKL OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1TKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tkl]] is a 2 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=1TKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TKL FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1tk1\|1tk1]], [[1tlb\|1tlb]]</div></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]] 2Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=4932 ATCC 18824])</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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [https://pdbe.org/1tkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [https://www.ebi.ac.uk/pdbsum/1tkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkl 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/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [~~http~~://pdbe.org/1tkl PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1tkl PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkl ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/HEM6_YEAST HEM6_YEAST]] Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX (By similarity).	+	[https://www.uniprot.org/uniprot/HEM6_YEAST HEM6_YEAST] Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 19:
	</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=1tkl 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=1tkl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Coproporphyrinogen oxidase (CPO) is an essential enzyme that catalyzes the sixth step of the heme biosynthetic pathway. Unusually for heme biosynthetic enzymes, CPO exists in two evolutionarily and mechanistically distinct families, with eukaryotes and some prokaryotes employing members of the highly conserved oxygen-dependent CPO family. Here, we report the crystal structure of the oxygen-dependent CPO from Saccharomyces cerevisiae (Hem13p), which was determined by optimized sulfur anomalous scattering and refined to a resolution of 2.0 A. The protein adopts a novel structure that is quite different from predicted models and features a central flat seven-stranded anti-parallel sheet that is flanked by helices. The dimeric assembly, which is seen in different crystal forms, is formed by packing of helices and a short isolated strand that forms a beta-ladder with its counterpart in the partner subunit. The deep active-site cleft is lined by conserved residues and has been captured in open and closed conformations in two different crystal forms. A substratesized cavity is completely buried in the closed conformation by the approximately 8-A movement of a helix that forms a lid over the active site. The structure therefore suggests residues that likely play critical roles in catalysis and explains the deleterious effect of many of the mutations associated with the disease hereditary coproporphyria.
-
-	Crystal structure of the oxygen-dependant coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae.,Phillips JD, Whitby FG, Warby CA, Labbe P, Yang C, Pflugrath JW, Ferrara JD, Robinson H, Kushner JP, Hill CP J Biol Chem. 2004 Sep 10;279(37):38960-8. Epub 2004 Jun 12. PMID:15194705<ref>PMID:15194705</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1tkl" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 18824]]
-	[[Category: Coproporphyrinogen oxidase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Ferrara~~, J D~~]]	+	[[Category: Saccharomyces cerevisiae]]
-	[[Category: Hill~~, C P~~]]	+	[[Category: Ferrara JD]]
-	[[Category: Kushner~~, J P~~]]	+	[[Category: Hill CP]]
-	[[Category: Labbe, P]]	+	[[Category: Kushner JP]]
-	[[Category: Pflugrath~~, J W~~]]	+	[[Category: Labbe P]]
-	[[Category: Phillips~~, J D~~]]	+	[[Category: Pflugrath JW]]
-	[[Category: Robinson, H]]	+	[[Category: Phillips JD]]
-	[[Category: Warby~~, C A~~]]	+	[[Category: Robinson H]]
-	[[Category: Whitby~~, F G~~]]	+	[[Category: Warby CA]]
-	[[Category: Yang, C]]	+	[[Category: Whitby FG]]
-	~~[[Category: Enzyme]]~~	+	[[Category: Yang C]]
-	~~[[Category: Heme biosynthesis]]~~	+
-	~~[[Category: Oxidoreductase~~]]	+

OCA at 11:54, 24 December 2020

2020-12-24T11:54:04Z

←Older revision		Revision as of 11:54, 24 December 2020
Line 1:		Line 1:

	==Yeast Oxygen-Dependent Coproporphyrinogen Oxidase==		==Yeast Oxygen-Dependent Coproporphyrinogen Oxidase==
-	<StructureSection load='1tkl' size='340' side='right' caption='[[1tkl]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1tkl' size='340' side='right'caption='[[1tkl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tkl]] is a 2 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=1TKL OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tkl]] is a 2 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=1TKL OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1TKL FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tlb\|1tlb]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1tk1\|1tk1]], [[1tlb\|1tlb]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [http://pdbe.org/1tkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [http://www.ebi.ac.uk/pdbsum/1tkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkl ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [http://pdbe.org/1tkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [http://www.ebi.ac.uk/pdbsum/1tkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 36:		Line 36:
	[[Category: Atcc 18824]]		[[Category: Atcc 18824]]
	[[Category: Coproporphyrinogen oxidase]]		[[Category: Coproporphyrinogen oxidase]]
		+	[[Category: Large Structures]]
	[[Category: Ferrara, J D]]		[[Category: Ferrara, J D]]
	[[Category: Hill, C P]]		[[Category: Hill, C P]]

OCA at 08:34, 21 March 2018

2018-03-21T08:34:42Z

←Older revision		Revision as of 08:34, 21 March 2018
Line 1:		Line 1:
		+
	==Yeast Oxygen-Dependent Coproporphyrinogen Oxidase==		==Yeast Oxygen-Dependent Coproporphyrinogen Oxidase==
	<StructureSection load='1tkl' size='340' side='right' caption='[[1tkl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1tkl' size='340' side='right' caption='[[1tkl]], [[Resolution\|resolution]] 2.00Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [http://pdbe.org/1tkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [http://www.ebi.ac.uk/pdbsum/1tkl 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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [http://pdbe.org/1tkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [http://www.ebi.ac.uk/pdbsum/1tkl PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tkl ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tk/1tkl_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tk/1tkl_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>

OCA at 16:25, 8 February 2016

2016-02-08T16:25:19Z

←Older revision		Revision as of 16:25, 8 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=1tkl ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 13:22, 10 September 2015

2015-09-10T13:22:23Z

←Older revision		Revision as of 13:22, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1tkl' size='340' side='right' caption='[[1tkl]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1tkl' size='340' side='right' caption='[[1tkl]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tkl]] is a 2 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=1TKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKL FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tkl]] is a 2 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=1TKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKL FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tlb\|1tlb]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tlb\|1tlb]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ~~Saccharomyces cerevisiae~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 ATCC 18824])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [http://www.ebi.ac.uk/pdbsum/1tkl 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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [http://pdbe.org/1tkl PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [http://www.ebi.ac.uk/pdbsum/1tkl 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 1tkl" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Atcc 18824]]
	[[Category: Coproporphyrinogen oxidase]]		[[Category: Coproporphyrinogen oxidase]]
-	[[Category: Saccharomyces cerevisiae]]
	[[Category: Ferrara, J D]]		[[Category: Ferrara, J D]]
	[[Category: Hill, C P]]		[[Category: Hill, C P]]

OCA at 00:37, 25 December 2014

2014-12-25T00:37:43Z

←Older revision		Revision as of 00:37, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tkl]] is a 2 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=1TKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKL FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tkl]] is a 2 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=1TKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKL FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tlb\|1tlb]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tlb\|1tlb]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [http://www.ebi.ac.uk/pdbsum/1tkl 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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [http://www.ebi.ac.uk/pdbsum/1tkl PDBsum]</span></td></tr>
-	<table>	+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/HEM6_YEAST HEM6_YEAST]] Involved in the heme biosynthesis. Catalyzes the aerobic oxidative decarboxylation of propionate groups of rings A and B of coproporphyrinogen-III to yield the vinyl groups in protoporphyrinogen-IX (By similarity).
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Coproporphyrinogen oxidase]]		[[Category: Coproporphyrinogen oxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Ferrara, J D.]]	+	[[Category: Ferrara, J D]]
-	[[Category: Hill, C P.]]	+	[[Category: Hill, C P]]
-	[[Category: Kushner, J P.]]	+	[[Category: Kushner, J P]]
-	[[Category: Labbe, P.]]	+	[[Category: Labbe, P]]
-	[[Category: Pflugrath, J W.]]	+	[[Category: Pflugrath, J W]]
-	[[Category: Phillips, J D.]]	+	[[Category: Phillips, J D]]
-	[[Category: Robinson, H.]]	+	[[Category: Robinson, H]]
-	[[Category: Warby, C A.]]	+	[[Category: Warby, C A]]
-	[[Category: Whitby, F G.]]	+	[[Category: Whitby, F G]]
-	[[Category: Yang, C~~.]]~~	+	[[Category: Yang, C]]
-	~~[[Category: Coproporphyrinogen oxidase~~]]	+
	[[Category: Enzyme]]		[[Category: Enzyme]]
	[[Category: Heme biosynthesis]]		[[Category: Heme biosynthesis]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 20:24, 29 September 2014

2014-09-29T20:24:10Z

←Older revision		Revision as of 20:24, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1tkl.~~png~~\|~~left~~\|200px]]	+	==Yeast Oxygen-Dependent Coproporphyrinogen Oxidase==
		+	<StructureSection load='1tkl' size='340' side='right' caption='[[1tkl]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1tkl]] is a 2 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=1TKL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TKL FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tlb\|1tlb]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">HEM13, YDR044W, YD5112.02 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Coproporphyrinogen_oxidase Coproporphyrinogen oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.3.3.3 1.3.3.3] </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=1tkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tkl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tkl RCSB], [http://www.ebi.ac.uk/pdbsum/1tkl 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/tk/1tkl_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 ==
		+	Coproporphyrinogen oxidase (CPO) is an essential enzyme that catalyzes the sixth step of the heme biosynthetic pathway. Unusually for heme biosynthetic enzymes, CPO exists in two evolutionarily and mechanistically distinct families, with eukaryotes and some prokaryotes employing members of the highly conserved oxygen-dependent CPO family. Here, we report the crystal structure of the oxygen-dependent CPO from Saccharomyces cerevisiae (Hem13p), which was determined by optimized sulfur anomalous scattering and refined to a resolution of 2.0 A. The protein adopts a novel structure that is quite different from predicted models and features a central flat seven-stranded anti-parallel sheet that is flanked by helices. The dimeric assembly, which is seen in different crystal forms, is formed by packing of helices and a short isolated strand that forms a beta-ladder with its counterpart in the partner subunit. The deep active-site cleft is lined by conserved residues and has been captured in open and closed conformations in two different crystal forms. A substratesized cavity is completely buried in the closed conformation by the approximately 8-A movement of a helix that forms a lid over the active site. The structure therefore suggests residues that likely play critical roles in catalysis and explains the deleterious effect of many of the mutations associated with the disease hereditary coproporphyria.

-	~~{{STRUCTURE_1tkl\| PDB=1tkl \| SCENE= }}~~	+	Crystal structure of the oxygen-dependant coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae.,Phillips JD, Whitby FG, Warby CA, Labbe P, Yang C, Pflugrath JW, Ferrara JD, Robinson H, Kushner JP, Hill CP J Biol Chem. 2004 Sep 10;279(37):38960-8. Epub 2004 Jun 12. PMID:15194705<ref>PMID:15194705</ref>

-	~~===Yeast Oxygen-Dependent Coproporphyrinogen Oxidase===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15194705}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1tkl]] is~~ a ~~2 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=1TKL OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015194705<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Coproporphyrinogen oxidase]]		[[Category: Coproporphyrinogen oxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]

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

2013-01-05T11:05:10Z

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

←Older revision

Revision as of 11:05, 5 January 2013

OCA at 11:05, 5 January 2013

2013-01-05T11:05:08Z

←Older revision		Revision as of 11:05, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1tkl.png\|left\|200px]]		[[Image:1tkl.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1tkl", 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_1tkl\| PDB=1tkl \| SCENE= }}		{{STRUCTURE_1tkl\| PDB=1tkl \| SCENE= }}

	===Yeast Oxygen-Dependent Coproporphyrinogen Oxidase===		===Yeast Oxygen-Dependent Coproporphyrinogen Oxidase===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15194705}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15194705 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15194705}}		{{ABSTRACT_PUBMED_15194705}}

	==About this Structure==		==About this Structure==
-	~~1TKL~~ is a 2 ~~chains~~ structure ~~of sequences~~ 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=1TKL OCA].	+	[[1tkl]] is a 2 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=1TKL OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15194705~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015194705</ref><references group="xtra"/>
	[[Category: Coproporphyrinogen oxidase]]		[[Category: Coproporphyrinogen oxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
Line 39:		Line 27:
	[[Category: Enzyme]]		[[Category: Enzyme]]
	[[Category: Heme biosynthesis]]		[[Category: Heme biosynthesis]]
-		+	[[Category: Oxidoreductase]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Tue Feb 17 00:25:35 2009''~~	+

OCA at 22:25, 16 February 2009

2009-02-16T22:25:36Z

←Older revision		Revision as of 22:25, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1TKL is a ~~[[Single protein]]~~ structure of ~~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=1TKL OCA].	+	1TKL is a 2 chains structure of sequences 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=1TKL OCA].

	==Reference==		==Reference==
-	Crystal structure of the oxygen-dependant coproporphyrinogen oxidase (Hem13p) of Saccharomyces cerevisiae., Phillips JD, Whitby FG, Warby CA, Labbe P, Yang C, Pflugrath JW, Ferrara JD, Robinson H, Kushner JP, Hill CP, J Biol Chem. 2004 Sep 10;279(37):38960-8. Epub 2004 Jun 12. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/15194705 15194705]~~	+	<ref group="xtra">PMID:15194705</ref><references group="xtra"/>
	[[Category: Coproporphyrinogen oxidase]]		[[Category: Coproporphyrinogen oxidase]]
	[[Category: Saccharomyces cerevisiae]]		[[Category: Saccharomyces cerevisiae]]
-	[[Category: Single protein]]
	[[Category: Ferrara, J D.]]		[[Category: Ferrara, J D.]]
	[[Category: Hill, C P.]]		[[Category: Hill, C P.]]
Line 41:		Line 40:
	[[Category: Heme biosynthesis]]		[[Category: Heme biosynthesis]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Mon Jul 28 04~~:50:~~13 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 00:25:35 2009''