2dd4 - Revision history

OCA at 13:47, 13 March 2024

2024-03-13T13:47:16Z

← Older revision		Revision as of 13:47, 13 March 2024
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	<StructureSection load='2dd4' size='340' side='right'caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2dd4' size='340' side='right'caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacterium_thiocyanoxidans"_happold_and_key_1937 "bacterium thiocyanoxidans" happold and key 1937~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Thiobacillus_thioparus Thiobacillus thioparus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>~~, ~~<scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</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]] 2.06Å</td></tr>
	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max-height: 3em;~~'>~~[[2dd5\|2dd5]]~~</~~div~~><~~/td></tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8]~~ </~~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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [https://pdbe.org/2dd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [https://www.ebi.ac.uk/pdbsum/2dd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd4 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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [https://pdbe.org/2dd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [https://www.ebi.ac.uk/pdbsum/2dd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[https://www.uniprot.org/uniprot/SCNA_THITI SCNA_THITI]] Involved in the degradation of thiocyanate. [[https://www.uniprot.org/uniprot/SCNC_THITI SCNC_THITI]] Involved in the degradation of thiocyanate. [[https://www.uniprot.org/uniprot/SCNB_THITI SCNB_THITI]] Involved in the degradation of thiocyanate.		[https://www.uniprot.org/uniprot/SCNA_THITI SCNA_THITI] Involved in the degradation of thiocyanate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dd4 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=2dd4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	Thiocyanate hydrolase (SCNase) of Thiobacillus thioparus THI115 is a cobalt(III)-containing enzyme catalyzing the degradation of thiocyanate to carbonyl sulfide and ammonia. We determined the crystal structures of the apo- and native SCNases at a resolution of 2.0 A. SCNases in both forms had a conserved hetero-dodecameric structure, (alphabetagamma)(4). Four alphabetagamma hetero-trimers were structurally equivalent. One alphabetagamma hetero-trimer was composed of the core domain and the betaN domain, which was located at the center of the molecule and linked the hetero-trimers with novel quaternary interfaces. In both the apo- and native SCNases, the core domain was structurally conserved between those of iron and cobalt-types of nitrile hydratase (NHase). Native SCNase possessed the post-translationally modified cysteine ligands, gammaCys131-SO(2)H and gammaCys133-SOH like NHases. However, the low-spin cobalt(III) was found to be in the distorted square-pyramidal geometry, which had not been reported before in any protein. The size as well as the electrostatic properties of the substrate-binding pocket was totally different from NHases with respect to the charge distribution and the substrate accessibility, which rationally explains the differences in the substrate preference between SCNase and NHase.

	Structure of thiocyanate hydrolase: a new nitrile hydratase family protein with a novel five-coordinate cobalt(III) center.,Arakawa T, Kawano Y, Kataoka S, Katayama Y, Kamiya N, Yohda M, Odaka M J Mol Biol. 2007 Mar 9;366(5):1497-509. Epub 2006 Dec 8. PMID:17222425<ref>PMID:17222425</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 2dd4" style="background-color:#fffaf0;"></div>~~
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	~~[[Category: Bacterium thiocyanoxidans happold and key 1937]]~~
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: ~~Thiocyanate hydrolase~~]]		[[Category: Thiobacillus thioparus]]
	[[Category: Arakawa, T]]		[[Category: Arakawa T]]
	[[Category: Kamiya, N]]		[[Category: Kamiya N]]
	[[Category: Kataoka, S]]		[[Category: Kataoka S]]
	[[Category: Katayama, Y]]		[[Category: Katayama Y]]
	[[Category: Kawano, Y]]		[[Category: Kawano Y]]
	[[Category: Odaka, M]]		[[Category: Odaka M]]
	[[Category: Yohda, M]]		[[Category: Yohda M]]
	~~[[Category: Carbonyl sulfide]]~~
	~~[[Category: Claw setting]]~~
	~~[[Category: Cobalt]]~~
	~~[[Category: Complex]]~~
	~~[[Category: Enzyme]]~~
	~~[[Category: Hydrolase]]~~
	~~[[Category: Metalloprotein]]~~
	~~[[Category: Model complex]]~~
	~~[[Category: Nitrile hydratase]]~~
	~~[[Category: Non-corrin]]~~
	~~[[Category: Protein]]~~
	~~[[Category: Sulfenic acid]]~~
	~~[[Category: Sulfinic acid]]~~
	~~[[Category: Thiocyanate~~]]

OCA at 07:24, 14 April 2021

2021-04-14T07:24:49Z

← Older revision		Revision as of 07:24, 14 April 2021
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	<StructureSection load='2dd4' size='340' side='right'caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2dd4' size='340' side='right'caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacterium_thiocyanoxidans"_happold_and_key_1937 "bacterium thiocyanoxidans" happold and key 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacterium_thiocyanoxidans"_happold_and_key_1937 "bacterium thiocyanoxidans" happold and key 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2dd5\|2dd5]]</div></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [~~http~~://pdbe.org/2dd4 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/2dd4 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd4 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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [https://pdbe.org/2dd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [https://www.ebi.ac.uk/pdbsum/2dd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd4 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[~~http~~://www.uniprot.org/uniprot/SCNA_THITI SCNA_THITI]] Involved in the degradation of thiocyanate. [[~~http~~://www.uniprot.org/uniprot/SCNC_THITI SCNC_THITI]] Involved in the degradation of thiocyanate. [[~~http~~://www.uniprot.org/uniprot/SCNB_THITI SCNB_THITI]] Involved in the degradation of thiocyanate.		[[https://www.uniprot.org/uniprot/SCNA_THITI SCNA_THITI]] Involved in the degradation of thiocyanate. [[https://www.uniprot.org/uniprot/SCNC_THITI SCNC_THITI]] Involved in the degradation of thiocyanate. [[https://www.uniprot.org/uniprot/SCNB_THITI SCNB_THITI]] Involved in the degradation of thiocyanate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 06:03, 10 July 2019

2019-07-10T06:03:45Z

← Older revision		Revision as of 06:03, 10 July 2019
Line 1:		Line 1:

	==Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme==		==Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme==
	<StructureSection load='2dd4' size='340' side='right' caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2dd4' size='340' side='right'caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_thiocyanoxidans"_happold_and_key_1937 "bacterium thiocyanoxidans" happold and key 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_thiocyanoxidans"_happold_and_key_1937 "bacterium thiocyanoxidans" happold and key 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=~~TAR~~:D(-)-TARTARIC+ACID'>~~TAR~~</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TLA:L(+)-TARTARIC+ACID'>TLA</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </span></td></tr>
Line 35:		Line 35:
	</StructureSection>		</StructureSection>
	[[Category: Bacterium thiocyanoxidans happold and key 1937]]		[[Category: Bacterium thiocyanoxidans happold and key 1937]]
			[[Category: Large Structures]]
	[[Category: Thiocyanate hydrolase]]		[[Category: Thiocyanate hydrolase]]
	[[Category: Arakawa, T]]		[[Category: Arakawa, T]]

OCA at 06:29, 30 May 2018

2018-05-30T06:29:44Z

← Older revision		Revision as of 06:29, 30 May 2018
Line 1:		Line 1:

	==Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme==		==Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme==
	<StructureSection load='2dd4' size='340' side='right' caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2dd4' size='340' side='right' caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>
Line 6:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [http://pdbe.org/2dd4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [http://www.ebi.ac.uk/pdbsum/2dd4 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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [http://pdbe.org/2dd4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [http://www.ebi.ac.uk/pdbsum/2dd4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2dd4 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/dd/2dd4_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dd/2dd4_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 22:15, 9 February 2016

2016-02-09T22:15:52Z

← Older revision		Revision as of 22:15, 9 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2dd4 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 02:33, 11 September 2015

2015-09-11T02:33:37Z

← Older revision		Revision as of 02:33, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='2dd4' size='340' side='right' caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>		<StructureSection load='2dd4' size='340' side='right' caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thiobacillus_thioparus Thiobacillus thioparus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacterium_thiocyanoxidans"_happold_and_key_1937 "bacterium thiocyanoxidans" happold and key 1937]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [http://www.ebi.ac.uk/pdbsum/2dd4 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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [http://pdbe.org/2dd4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [http://www.ebi.ac.uk/pdbsum/2dd4 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 2dd4" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Thiobacillus thioparus~~]]		[[Category: Bacterium thiocyanoxidans happold and key 1937]]
	[[Category: Thiocyanate hydrolase]]		[[Category: Thiocyanate hydrolase]]
	[[Category: Arakawa, T]]		[[Category: Arakawa, T]]

OCA at 09:53, 25 December 2014

2014-12-25T09:53:48Z

← Older revision		Revision as of 09:53, 25 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thiobacillus_thioparus Thiobacillus thioparus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>		<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thiobacillus_thioparus Thiobacillus thioparus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [http://www.ebi.ac.uk/pdbsum/2dd4 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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [http://www.ebi.ac.uk/pdbsum/2dd4 PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/SCNA_THITI SCNA_THITI]] Involved in the degradation of thiocyanate. [[http://www.uniprot.org/uniprot/SCNC_THITI SCNC_THITI]] Involved in the degradation of thiocyanate. [[http://www.uniprot.org/uniprot/SCNB_THITI SCNB_THITI]] Involved in the degradation of thiocyanate.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Thiobacillus thioparus]]		[[Category: Thiobacillus thioparus]]
	[[Category: Thiocyanate hydrolase]]		[[Category: Thiocyanate hydrolase]]
	[[Category: Arakawa, T.]]		[[Category: Arakawa, T]]
	[[Category: Kamiya, N.]]		[[Category: Kamiya, N]]
	[[Category: Kataoka, S.]]		[[Category: Kataoka, S]]
	[[Category: Katayama, Y.]]		[[Category: Katayama, Y]]
	[[Category: Kawano, Y.]]		[[Category: Kawano, Y]]
	[[Category: Odaka, M.]]		[[Category: Odaka, M]]
	[[Category: Yohda, M.]]		[[Category: Yohda, M]]
	[[Category: Carbonyl sulfide]]		[[Category: Carbonyl sulfide]]
	[[Category: Claw setting]]		[[Category: Claw setting]]

OCA at 01:02, 30 September 2014

2014-09-30T01:02:34Z

← Older revision		Revision as of 01:02, 30 September 2014
Line 1:		Line 1:
	[[Image:~~2dd4~~.~~png~~\|~~left~~\|~~200px~~]]		==Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme==
			<StructureSection load='2dd4' size='340' side='right' caption='[[2dd4]], [[Resolution\|resolution]] 2.06Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[2dd4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thiobacillus_thioparus Thiobacillus thioparus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2DD4 FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FRU:FRUCTOSE'>FRU</scene>, <scene name='pdbligand=TAR:D(-)-TARTARIC+ACID'>TAR</scene><br>
			<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[2dd5\|2dd5]]</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Thiocyanate_hydrolase Thiocyanate hydrolase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.5.8 3.5.5.8] </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=2dd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2dd4 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2dd4 RCSB], [http://www.ebi.ac.uk/pdbsum/2dd4 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/dd/2dd4_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 ==
			Thiocyanate hydrolase (SCNase) of Thiobacillus thioparus THI115 is a cobalt(III)-containing enzyme catalyzing the degradation of thiocyanate to carbonyl sulfide and ammonia. We determined the crystal structures of the apo- and native SCNases at a resolution of 2.0 A. SCNases in both forms had a conserved hetero-dodecameric structure, (alphabetagamma)(4). Four alphabetagamma hetero-trimers were structurally equivalent. One alphabetagamma hetero-trimer was composed of the core domain and the betaN domain, which was located at the center of the molecule and linked the hetero-trimers with novel quaternary interfaces. In both the apo- and native SCNases, the core domain was structurally conserved between those of iron and cobalt-types of nitrile hydratase (NHase). Native SCNase possessed the post-translationally modified cysteine ligands, gammaCys131-SO(2)H and gammaCys133-SOH like NHases. However, the low-spin cobalt(III) was found to be in the distorted square-pyramidal geometry, which had not been reported before in any protein. The size as well as the electrostatic properties of the substrate-binding pocket was totally different from NHases with respect to the charge distribution and the substrate accessibility, which rationally explains the differences in the substrate preference between SCNase and NHase.

	~~{{STRUCTURE_2dd4\| PDB=2dd4 \| SCENE= }}~~		Structure of thiocyanate hydrolase: a new nitrile hydratase family protein with a novel five-coordinate cobalt(III) center.,Arakawa T, Kawano Y, Kataoka S, Katayama Y, Kamiya N, Yohda M, Odaka M J Mol Biol. 2007 Mar 9;366(5):1497-509. Epub 2006 Dec 8. PMID:17222425<ref>PMID:17222425</ref>

	~~===Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_17222425}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[2dd4]] is~~ a ~~12 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thiobacillus_thioparus Thiobacillus thioparus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:017222425<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Thiobacillus thioparus]]		[[Category: Thiobacillus thioparus]]
	[[Category: Thiocyanate hydrolase]]		[[Category: Thiocyanate hydrolase]]

OCA: Protected "2dd4" [edit=sysop:move=sysop]

2013-01-06T10:19:47Z

Protected "2dd4" [edit=sysop:move=sysop]

← Older revision	Revision as of 10:19, 6 January 2013
(No difference)

OCA at 10:19, 6 January 2013

2013-01-06T10:19:44Z

← Older revision		Revision as of 10:19, 6 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:2dd4.png\|left\|200px]]		[[Image:2dd4.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_2dd4", 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_2dd4\| PDB=2dd4 \| SCENE= }}		{{STRUCTURE_2dd4\| PDB=2dd4 \| SCENE= }}

	===Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme===		===Thiocyanate hydrolase (SCNase) from Thiobacillus thioparus recombinant apo-enzyme===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_17222425}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 17222425 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_17222425}}		{{ABSTRACT_PUBMED_17222425}}

	==About this Structure==		==About this Structure==
	~~2DD4~~ is a 12 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thiobacillus_thioparus Thiobacillus thioparus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA].		[[2dd4]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Thiobacillus_thioparus Thiobacillus thioparus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DD4 OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~17222425~~</ref><references group="xtra"/>		<ref group="xtra">PMID:017222425</ref><references group="xtra"/>
	[[Category: Thiobacillus thioparus]]		[[Category: Thiobacillus thioparus]]
	[[Category: Thiocyanate hydrolase]]		[[Category: Thiocyanate hydrolase]]
Line 47:		Line 35:
	[[Category: Sulfinic acid]]		[[Category: Sulfinic acid]]
	[[Category: Thiocyanate]]		[[Category: Thiocyanate]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Feb 17 13:09:48 2009''~~