1tlb - Revision history

OCA at 08:40, 14 February 2024

2024-02-14T08:40:15Z

←Older revision		Revision as of 08:40, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1tlb' size='340' side='right'caption='[[1tlb]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1tlb' size='340' side='right'caption='[[1tlb]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tlb]] is a 6 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=1TLB OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1TLB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tlb]] is a 6 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=1TLB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TLB FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 2.4Å</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]]~~, [[~~1tkl~~\|~~1tkl~~]]~~</div>~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [https://pdbe.org/1tlb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [https://www.ebi.ac.uk/pdbsum/1tlb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tlb 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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [~~http~~://pdbe.org/1tlb PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1tlb PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1tlb 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 22:		Line 20:
	</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=1tlb 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=1tlb 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 1tlb" 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: Phillip~~, J D~~]]	+	[[Category: Pflugrath JW]]
-	[[Category: Robinson, H]]	+	[[Category: Phillip 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

2020-12-24T11:54:55Z

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

	==Yeast coproporphyrinogen oxidase==		==Yeast coproporphyrinogen oxidase==
-	<StructureSection load='1tlb' size='340' side='right' caption='[[1tlb]], [[Resolution\|resolution]] 2.40Å' scene=''>	+	<StructureSection load='1tlb' size='340' side='right'caption='[[1tlb]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tlb]] is a 6 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=1TLB OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1TLB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tlb]] is a 6 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=1TLB OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1TLB FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tkl\|1tkl]]</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]], [[1tkl\|1tkl]]</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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [http://pdbe.org/1tlb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [http://www.ebi.ac.uk/pdbsum/1tlb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tlb 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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [http://pdbe.org/1tlb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [http://www.ebi.ac.uk/pdbsum/1tlb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tlb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 37:		Line 37:
	[[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 08:56, 21 March 2018

2018-03-21T08:56:30Z

←Older revision		Revision as of 08:56, 21 March 2018
Line 1:		Line 1:
		+
	==Yeast coproporphyrinogen oxidase==		==Yeast coproporphyrinogen oxidase==
	<StructureSection load='1tlb' size='340' side='right' caption='[[1tlb]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1tlb' size='340' side='right' caption='[[1tlb]], [[Resolution\|resolution]] 2.40Å' scene=''>
Line 7:		Line 8:
	<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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [http://pdbe.org/1tlb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [http://www.ebi.ac.uk/pdbsum/1tlb 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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [http://pdbe.org/1tlb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [http://www.ebi.ac.uk/pdbsum/1tlb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1tlb ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 15:		Line 16:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tl/1tlb_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/tl/1tlb_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 13:56, 9 February 2016

2016-02-09T13:56:06Z

←Older revision		Revision as of 13:56, 9 February 2016
Line 19:		Line 19:
	<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=1tlb ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 22:53, 10 September 2015

2015-09-10T22:53:34Z

←Older revision		Revision as of 22:53, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1tlb' size='340' side='right' caption='[[1tlb]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='1tlb' size='340' side='right' caption='[[1tlb]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1tlb]] is a 6 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=1TLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TLB FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1tlb]] is a 6 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=1TLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TLB FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tkl\|1tkl]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tkl\|1tkl]]</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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [http://www.ebi.ac.uk/pdbsum/1tlb 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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [http://pdbe.org/1tlb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [http://www.ebi.ac.uk/pdbsum/1tlb PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 29:		Line 29:
	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 1tlb" 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 07:13, 25 December 2014

2014-12-25T07:13:46Z

←Older revision		Revision as of 07:13, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1tlb]] is a 6 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=1TLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TLB FirstGlance]. <br>		<table><tr><td colspan='2'>[[1tlb]] is a 6 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=1TLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TLB FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tkl\|1tkl]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tkl\|1tkl]]</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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [http://www.ebi.ac.uk/pdbsum/1tlb 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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [http://www.ebi.ac.uk/pdbsum/1tlb 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 33:		Line 35:
	[[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: Phillip, J D.]]	+	[[Category: Phillip, 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 18:43, 29 September 2014

2014-09-29T18:43:46Z

←Older revision		Revision as of 18:43, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1tlb.~~png~~\|~~left~~\|200px]]	+	==Yeast coproporphyrinogen oxidase==
		+	<StructureSection load='1tlb' size='340' side='right' caption='[[1tlb]], [[Resolution\|resolution]] 2.40Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1tlb]] is a 6 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=1TLB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1TLB FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1tk1\|1tk1]], [[1tkl\|1tkl]]</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=1tlb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tlb OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1tlb RCSB], [http://www.ebi.ac.uk/pdbsum/1tlb 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/tl/1tlb_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_1tlb\| PDB=1tlb \| 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 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__
-	~~[[1tlb]] is~~ a ~~6 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=1TLB 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 "1tlb" [edit=sysop:move=sysop]

2013-01-05T11:27:49Z

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

←Older revision

Revision as of 11:27, 5 January 2013

OCA at 11:27, 5 January 2013

2013-01-05T11:27:47Z

←Older revision		Revision as of 11:27, 5 January 2013
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-	{{Seed}}
	[[Image:1tlb.png\|left\|200px]]		[[Image:1tlb.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1tlb", 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_1tlb\| PDB=1tlb \| SCENE= }}		{{STRUCTURE_1tlb\| PDB=1tlb \| SCENE= }}

	===Yeast coproporphyrinogen oxidase===		===Yeast 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==
-	~~1TLB~~ is a 6 ~~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=1TLB OCA].	+	[[1tlb]] is a 6 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=1TLB 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 10:17:49 2009''~~	+

OCA at 08:17, 17 February 2009

2009-02-17T08:17:50Z

←Older revision		Revision as of 08:17, 17 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	1TLB 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=1TLB OCA].	+	1TLB is a 6 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=1TLB 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 14~~:05:~~56 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 10:17:49 2009''