2oyy - Revision history

OCA at 09:06, 21 February 2024

2024-02-21T09:06:59Z

←Older revision		Revision as of 09:06, 21 February 2024
Line 3:		Line 3:
	<StructureSection load='2oyy' size='340' side='right'caption='[[2oyy]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2oyy' size='340' side='right'caption='[[2oyy]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oyy]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_700808 Atcc 700808~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oyy]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Ruegeria_pomeroyi Ruegeria pomeroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OYY 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>~~, ~~<scene name='pdbligand=IOD:IODIDE+ION'>IOD</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]] 2.5Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~spoa0176 ([https~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=89184 ATCC 700808])~~</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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [https://pdbe.org/2oyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [https://www.ebi.ac.uk/pdbsum/2oyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oyy 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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [https://pdbe.org/2oyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [https://www.ebi.ac.uk/pdbsum/2oyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oyy ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/Q5LL55_RUEPO Q5LL55_RUEPO]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 18:		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=2oyy 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=2oyy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	We have cloned, expressed, isolated and characterized a hexameric tyrosine-coordinated heme protein (HTHP) from the marine bacterium Silicibacter pomeroyi. HTHP shows peroxidase and catalase activity and has a high thermal stability. As-isolated HTHP has absorption maxima at 407, 495, 504, 532 and 622 nm wavelength. Upon reduction maxima at 430, 564 and 596 nm wavelength are discernible. The crystal structure of HTHP reveals a hexameric, ring-like arrangement of six monomers. Each monomer binds a solvent accessible heme group, which is stabilized by the interaction of three neighboring monomers. The pocket around the heme distal side is positively charged due to three conserved arginine residues in direct vicinity. The heme iron is penta-coordinated with a tyrosine residue as proximal ligand. The coordinating hydroxyl-group of the tyrosine ligand interacts with the guanidinium group of a nearby arginine residue, an arrangement closely resembling the catalytic dyad found in monofunctional heme-containing catalases and coral allene oxide synthases, which are b-type cytochromes with tyrosine coordination trans to an empty coordination site. Despite the similarity in heme coordination HTHP is functionally and structurally unrelated to catalases and other heme-containing proteins. Its hexameric arrangement, solvent accessible heme binding pocket and heme coordination by tyrosine render HTHP a unique protein with unusual properties. A database search against complete and incomplete genomes shows that the 76 amino acid residues sequence of HTHP is unrelated to characterized proteins, but is homologous to orfs found in a phylogenetically diverse set of bacteria with sequence identities of 30-76%. We therefore propose that HTHP is the prototype of a new class of heme proteins.
-
-	HTHP: a novel class of hexameric, tyrosine-coordinated heme proteins.,Jeoung JH, Pippig DA, Martins BM, Wagener N, Dobbek H J Mol Biol. 2007 May 11;368(4):1122-31. Epub 2007 Mar 6. PMID:17395199<ref>PMID:17395199</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 2oyy" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: Atcc 700808]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Dobbek, H~~]]	+	[[Category: Ruegeria pomeroyi]]
-	[[Category: ~~All helical]]~~	+	[[Category: Dobbek H]]
-	~~[[Category: Unknown function~~]]	+

OCA at 13:09, 9 June 2021

2021-06-09T13:09:39Z

←Older revision		Revision as of 13:09, 9 June 2021
Line 1:		Line 1:

	==HTHP: a hexameric tyrosine-coordinated heme protein==		==HTHP: a hexameric tyrosine-coordinated heme protein==
-	<StructureSection load='2oyy' size='340' side='right' caption='[[2oyy]], [[Resolution\|resolution]] 2.50Å' scene=''>	+	<StructureSection load='2oyy' size='340' side='right'caption='[[2oyy]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oyy]] is a 8 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_700808 Atcc 700808]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2OYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oyy]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_700808 Atcc 700808]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OYY 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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spoa0176 ([~~http~~://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89184 ATCC 700808])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spoa0176 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89184 ATCC 700808])</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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [~~http~~://pdbe.org/2oyy PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2oyy PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2oyy 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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [https://pdbe.org/2oyy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [https://www.ebi.ac.uk/pdbsum/2oyy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2oyy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oy/2oyy_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/oy/2oyy_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
Line 32:		Line 32:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 700808]]		[[Category: Atcc 700808]]
		+	[[Category: Large Structures]]
	[[Category: Dobbek, H]]		[[Category: Dobbek, H]]
	[[Category: All helical]]		[[Category: All helical]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 09:13, 18 October 2017

2017-10-18T09:13:41Z

←Older revision		Revision as of 09:13, 18 October 2017
Line 1:		Line 1:
		+
	==HTHP: a hexameric tyrosine-coordinated heme protein==		==HTHP: a hexameric tyrosine-coordinated heme protein==
	<StructureSection load='2oyy' size='340' side='right' caption='[[2oyy]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2oyy' size='340' side='right' caption='[[2oyy]], [[Resolution\|resolution]] 2.50Å' scene=''>
Line 5:		Line 6:
	</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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spoa0176 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89184 ATCC 700808])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spoa0176 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89184 ATCC 700808])</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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [http://pdbe.org/2oyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [http://www.ebi.ac.uk/pdbsum/2oyy 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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [http://pdbe.org/2oyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [http://www.ebi.ac.uk/pdbsum/2oyy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2oyy ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==

OCA at 14:18, 7 February 2016

2016-02-07T14:18:55Z

←Older revision		Revision as of 14:18, 7 February 2016
Line 15:		Line 15:
	<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=2oyy ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:18, 10 September 2015

2015-09-10T02:18:47Z

←Older revision		Revision as of 02:18, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='2oyy' size='340' side='right' caption='[[2oyy]], [[Resolution\|resolution]] 2.50Å' scene=''>		<StructureSection load='2oyy' size='340' side='right' caption='[[2oyy]], [[Resolution\|resolution]] 2.50Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[2oyy]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Ruegeria_pomeroyi Ruegeria pomeroyi~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OYY FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[2oyy]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_700808 Atcc 700808]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OYY 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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spoa0176 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89184 ~~Ruegeria pomeroyi~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spoa0176 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89184 ATCC 700808])</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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [http://www.ebi.ac.uk/pdbsum/2oyy 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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [http://pdbe.org/2oyy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [http://www.ebi.ac.uk/pdbsum/2oyy PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 25:		Line 25:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 2oyy" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Ruegeria pomeroyi~~]]	+	[[Category: Atcc 700808]]
	[[Category: Dobbek, H]]		[[Category: Dobbek, H]]
	[[Category: All helical]]		[[Category: All helical]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 15:52, 24 December 2014

2014-12-24T15:52:30Z

←Older revision		Revision as of 15:52, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2oyy]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ruegeria_pomeroyi Ruegeria pomeroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OYY FirstGlance]. <br>		<table><tr><td colspan='2'>[[2oyy]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ruegeria_pomeroyi Ruegeria pomeroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OYY 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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spoa0176 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89184 Ruegeria pomeroyi])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spoa0176 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89184 Ruegeria pomeroyi])</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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [http://www.ebi.ac.uk/pdbsum/2oyy 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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [http://www.ebi.ac.uk/pdbsum/2oyy 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 30:		Line 30:
	</StructureSection>		</StructureSection>
	[[Category: Ruegeria pomeroyi]]		[[Category: Ruegeria pomeroyi]]
-	[[Category: Dobbek, H.]]	+	[[Category: Dobbek, H]]
	[[Category: All helical]]		[[Category: All helical]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA at 19:13, 30 September 2014

2014-09-30T19:13:25Z

←Older revision		Revision as of 19:13, 30 September 2014
Line 1:		Line 1:
-	[[~~Image:~~2oyy.~~png~~\|~~left~~\|200px]]	+	==HTHP: a hexameric tyrosine-coordinated heme protein==
		+	<StructureSection load='2oyy' size='340' side='right' caption='[[2oyy]], [[Resolution\|resolution]] 2.50Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[2oyy]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ruegeria_pomeroyi Ruegeria pomeroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2OYY 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>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">spoa0176 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=89184 Ruegeria pomeroyi])</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=2oyy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oyy OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2oyy RCSB], [http://www.ebi.ac.uk/pdbsum/2oyy 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/oy/2oyy_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 ==
		+	We have cloned, expressed, isolated and characterized a hexameric tyrosine-coordinated heme protein (HTHP) from the marine bacterium Silicibacter pomeroyi. HTHP shows peroxidase and catalase activity and has a high thermal stability. As-isolated HTHP has absorption maxima at 407, 495, 504, 532 and 622 nm wavelength. Upon reduction maxima at 430, 564 and 596 nm wavelength are discernible. The crystal structure of HTHP reveals a hexameric, ring-like arrangement of six monomers. Each monomer binds a solvent accessible heme group, which is stabilized by the interaction of three neighboring monomers. The pocket around the heme distal side is positively charged due to three conserved arginine residues in direct vicinity. The heme iron is penta-coordinated with a tyrosine residue as proximal ligand. The coordinating hydroxyl-group of the tyrosine ligand interacts with the guanidinium group of a nearby arginine residue, an arrangement closely resembling the catalytic dyad found in monofunctional heme-containing catalases and coral allene oxide synthases, which are b-type cytochromes with tyrosine coordination trans to an empty coordination site. Despite the similarity in heme coordination HTHP is functionally and structurally unrelated to catalases and other heme-containing proteins. Its hexameric arrangement, solvent accessible heme binding pocket and heme coordination by tyrosine render HTHP a unique protein with unusual properties. A database search against complete and incomplete genomes shows that the 76 amino acid residues sequence of HTHP is unrelated to characterized proteins, but is homologous to orfs found in a phylogenetically diverse set of bacteria with sequence identities of 30-76%. We therefore propose that HTHP is the prototype of a new class of heme proteins.

-	~~{{STRUCTURE_2oyy\| PDB=2oyy \| SCENE= }}~~	+	HTHP: a novel class of hexameric, tyrosine-coordinated heme proteins.,Jeoung JH, Pippig DA, Martins BM, Wagener N, Dobbek H J Mol Biol. 2007 May 11;368(4):1122-31. Epub 2007 Mar 6. PMID:17395199<ref>PMID:17395199</ref>

-	~~===HTHP:~~ a ~~hexameric tyrosine-coordinated heme protein===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_17395199}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[2oyy]] is a 8 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Ruegeria_pomeroyi Ruegeria pomeroyi]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:017395199<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Ruegeria pomeroyi]]		[[Category: Ruegeria pomeroyi]]
	[[Category: Dobbek, H.]]		[[Category: Dobbek, H.]]
	[[Category: All helical]]		[[Category: All helical]]
	[[Category: Unknown function]]		[[Category: Unknown function]]

OCA: Protected "2oyy" [edit=sysop:move=sysop]

2013-01-07T14:10:06Z

Protected "2oyy" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:10, 7 January 2013

OCA at 14:10, 7 January 2013

2013-01-07T14:10:01Z

←Older revision		Revision as of 14:10, 7 January 2013
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-	{{Seed}}
	[[Image:2oyy.png\|left\|200px]]		[[Image:2oyy.png\|left\|200px]]

-	<!--
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	{{STRUCTURE_2oyy\| PDB=2oyy \| SCENE= }}		{{STRUCTURE_2oyy\| PDB=2oyy \| SCENE= }}

	===HTHP: a hexameric tyrosine-coordinated heme protein===		===HTHP: a hexameric tyrosine-coordinated heme protein===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_17395199}}, adds the Publication Abstract to the page
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	{{ABSTRACT_PUBMED_17395199}}		{{ABSTRACT_PUBMED_17395199}}

	==About this Structure==		==About this Structure==
-	~~2OYY~~ is a 8 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/~~Silicibacter_pomeroyi Silicibacter~~ pomeroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA].	+	[[2oyy]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Ruegeria_pomeroyi Ruegeria pomeroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~17395199~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:017395199</ref><references group="xtra"/>
-	[[Category: ~~Silicibacter~~ pomeroyi]]	+	[[Category: Ruegeria pomeroyi]]
	[[Category: Dobbek, H.]]		[[Category: Dobbek, H.]]
	[[Category: All helical]]		[[Category: All helical]]
-		+	[[Category: Unknown function]]
-	~~''Page seeded by~~ [~~http~~:~~//oca.weizmann.ac.il/oca OCA~~ ] ~~on Mon Feb 16 14:24:42 2009''~~	+

OCA at 12:24, 16 February 2009

2009-02-16T12:24:42Z

←Older revision		Revision as of 12:24, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
-	2OYY is a ~~[[Single protein]]~~ structure of ~~sequence~~ from [http://en.wikipedia.org/wiki/Silicibacter_pomeroyi Silicibacter pomeroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA].	+	2OYY is a 8 chains structure of sequences from [http://en.wikipedia.org/wiki/Silicibacter_pomeroyi Silicibacter pomeroyi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OYY OCA].

	==Reference==		==Reference==
-	~~HTHP: a novel class of hexameric, tyrosine-coordinated heme proteins., Jeoung JH, Pippig DA, Martins BM, Wagener N, Dobbek H, J Mol Biol. 2007 May 11;368(4):1122-31. Epub 2007 Mar 6.~~ PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/17395199 17395199]~~	+	<ref group="xtra">PMID:17395199</ref><references group="xtra"/>
	[[Category: Silicibacter pomeroyi]]		[[Category: Silicibacter pomeroyi]]
-	[[Category: Single protein]]
	[[Category: Dobbek, H.]]		[[Category: Dobbek, H.]]
	[[Category: All helical]]		[[Category: All helical]]

-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 17~~:01:~~56 2008~~''	+	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 14:24:42 2009''