1dw9 - Revision history

OCA at 09:54, 20 March 2024

OCA — Wed, 20 Mar 2024 09:54:45 GMT

←Older revision		Revision as of 09:54, 20 March 2024
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	<StructureSection load='1dw9' size='340' side='right'caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1dw9' size='340' side='right'caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/~~"bacillus_coli"_migula_1895 "bacillus~~ coli~~" migula 1895~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>~~, ~~<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]] 1.65Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=~~MSE~~:~~SELENOMETHIONINE~~'>~~MSE~~</scene><~~/td></tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <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"><div style='overflow: auto; max-height: 3em;~~'>~~[[1dwk\|1dwk]]~~</~~div~~><~~/td></tr>~~	+
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b></td><td class="sblockDat"><span class='plainlinks~~'>~~[https://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104]~~ </~~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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [https://pdbe.org/1dw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw9 ProSAT], [https://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [https://pdbe.org/1dw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw9 ProSAT], [https://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[https://www.uniprot.org/uniprot/CYNS_ECOLI CYNS_ECOLI]] Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide.	+	[https://www.uniprot.org/uniprot/CYNS_ECOLI CYNS_ECOLI] Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide.
	== 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=1dw9 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=1dw9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	BACKGROUND: Cyanase is an enzyme found in bacteria and plants that catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. In Escherichia coli, cyanase is induced from the cyn operon in response to extracellular cyanate. The enzyme is functionally active as a homodecamer of 17 kDa subunits, and displays half-site binding of substrates or substrate analogs. The enzyme shows no significant amino acid sequence homology with other proteins. RESULTS: We have determined the crystal structure of cyanase at 1.65 A resolution using the multiwavelength anomalous diffraction (MAD) method. Cyanase crystals are triclinic and contain one homodecamer in the asymmetric unit. Selenomethionine-labeled protein offers 40 selenium atoms for use in phasing. Structures of cyanase with bound chloride or oxalate anions, inhibitors of the enzyme, allowed identification of the active site. CONCLUSIONS: The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.
-
-	Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.,Walsh MA, Otwinowski Z, Perrakis A, Anderson PM, Joachimiak A Structure. 2000 May 15;8(5):505-14. PMID:10801492<ref>PMID:10801492</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1dw9" style="background-color:#fffaf0;"></div>
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus~~ coli ~~migula 1895]]~~	+	[[Category: Escherichia coli]]
-	~~[[Category: Cyanase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Anderson~~, P M~~]]	+	[[Category: Anderson PM]]
-	[[Category: Joachimiak, A]]	+	[[Category: Joachimiak A]]
-	~~[[Category: Structural genomic~~]]	+	[[Category: Otwinowski Z]]
-	[[Category: Otwinowski, Z]]	+	[[Category: Perrakis A]]
-	[[Category: Perrakis, A]]	+	[[Category: Walsh MA]]
-	[[Category: Walsh~~, M A]]~~	+
-	~~[[Category: Cyanate degradation]]~~	+
-	~~[[Category: Lyase]]~~	+
-	~~[[Category: Mcsg]]~~	+
-	~~[[Category: PSI, Protein structure initiative~~]]	+

OCA at 09:49, 26 May 2021

OCA — Wed, 26 May 2021 09:49:41 GMT

OCA at 11:29, 10 May 2019

OCA — Fri, 10 May 2019 11:29:11 GMT

←Older revision		Revision as of 11:29, 10 May 2019
Line 1:		Line 1:

	==Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site==		==Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site==
-	<StructureSection load='1dw9' size='340' side='right' caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>	+	<StructureSection load='1dw9' size='340' side='right'caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>
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	[[Category: Bacillus coli migula 1895]]		[[Category: Bacillus coli migula 1895]]
	[[Category: Cyanase]]		[[Category: Cyanase]]
		+	[[Category: Large Structures]]
	[[Category: Anderson, P M]]		[[Category: Anderson, P M]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 08:00, 13 December 2017

OCA — Wed, 13 Dec 2017 08:00:49 GMT

←Older revision		Revision as of 08:00, 13 December 2017
Line 1:		Line 1:
		+
	==Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site==		==Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site==
	<StructureSection load='1dw9' size='340' side='right' caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1dw9' size='340' side='right' caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>
Line 7:		Line 8:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dwk\|1dwk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dwk\|1dwk]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [http://pdbe.org/1dw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [http://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [http://pdbe.org/1dw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw9 ProSAT], [http://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</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/dw/1dw9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/dw/1dw9_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 18:17, 8 February 2016

OCA — Mon, 08 Feb 2016 18:17:34 GMT

←Older revision		Revision as of 18:17, 8 February 2016
Line 7:		Line 7:
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dwk\|1dwk]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dwk\|1dwk]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [http://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [http://pdbe.org/1dw9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [http://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	<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=1dw9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
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	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 1dw9" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:09, 22 April 2015

OCA — Wed, 22 Apr 2015 07:09:10 GMT

←Older revision		Revision as of 07:09, 22 April 2015
Line 1:		Line 1:
-	==~~STRUCTURE OF CYANASE REVEALS THAT A NOVEL DIMERIC AND DECAMERIC ARRANGEMENT OF SUBUNITS IS REQUIRED FOR FORMATION OF THE ENZYME ACTIVE SITE~~==	+	==Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site==
	<StructureSection load='1dw9' size='340' side='right' caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1dw9' size='340' side='right' caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Escherichia_coli Escherichia~~ coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
Line 33:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bacillus coli migula 1895]]
	[[Category: Cyanase]]		[[Category: Cyanase]]
-	[[Category: Escherichia coli]]
	[[Category: Anderson, P M]]		[[Category: Anderson, P M]]
	[[Category: Joachimiak, A]]		[[Category: Joachimiak, A]]

OCA at 01:14, 25 December 2014

OCA — Thu, 25 Dec 2014 01:14:53 GMT

←Older revision		Revision as of 01:14, 25 December 2014
Line 9:		Line 9:
	<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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [http://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [http://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CYNS_ECOLI CYNS_ECOLI]] Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 22:48, 22 December 2014

OCA — Mon, 22 Dec 2014 22:48:17 GMT

←Older revision		Revision as of 22:48, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>	+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dwk\|1dwk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dwk\|1dwk]]</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [http://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [http://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 33:		Line 33:
	[[Category: Cyanase]]		[[Category: Cyanase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]
-	[[Category: Anderson, P M.]]	+	[[Category: Anderson, P M]]
-	[[Category: Joachimiak, A.]]	+	[[Category: Joachimiak, A]]
-	[[Category: ~~Mcsg, Midwest Center for~~ Structural ~~Genomics.~~]]	+	[[Category: Structural genomic]]
-	[[Category: Otwinowski, Z.]]	+	[[Category: Otwinowski, Z]]
-	[[Category: Perrakis, A.]]	+	[[Category: Perrakis, A]]
-	[[Category: Walsh, M A.]]	+	[[Category: Walsh, M A]]
	[[Category: Cyanate degradation]]		[[Category: Cyanate degradation]]
	[[Category: Lyase]]		[[Category: Lyase]]
	[[Category: Mcsg]]		[[Category: Mcsg]]
-	[[Category: ~~Midwest center for structural genomic]]~~	+	[[Category: PSI, Protein structure initiative]]
-	~~[[Category:~~ Protein structure initiative]]	+
-	~~[[Category: Psi]]~~	+
-	~~[[Category: Structural genomic~~]]	+

OCA at 10:45, 3 October 2014

OCA — Fri, 03 Oct 2014 10:45:09 GMT

←Older revision		Revision as of 10:45, 3 October 2014
Line 1:		Line 1:
-	~~{{STRUCTURE_1dw9\| PDB=1dw9 \| SCENE= }}~~	+	==STRUCTURE OF CYANASE REVEALS THAT A NOVEL DIMERIC AND DECAMERIC ARRANGEMENT OF SUBUNITS IS REQUIRED FOR FORMATION OF THE ENZYME ACTIVE SITE==
-	===STRUCTURE OF CYANASE REVEALS THAT A NOVEL DIMERIC AND DECAMERIC ARRANGEMENT OF SUBUNITS IS REQUIRED FOR FORMATION OF THE ENZYME ACTIVE SITE===	+	<StructureSection load='1dw9' size='340' side='right' caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>
-	~~{{ABSTRACT_PUBMED_10801492}}~~	+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dwk\|1dwk]]</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [http://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [http://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</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/dw/1dw9_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 ==
		+	BACKGROUND: Cyanase is an enzyme found in bacteria and plants that catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide. In Escherichia coli, cyanase is induced from the cyn operon in response to extracellular cyanate. The enzyme is functionally active as a homodecamer of 17 kDa subunits, and displays half-site binding of substrates or substrate analogs. The enzyme shows no significant amino acid sequence homology with other proteins. RESULTS: We have determined the crystal structure of cyanase at 1.65 A resolution using the multiwavelength anomalous diffraction (MAD) method. Cyanase crystals are triclinic and contain one homodecamer in the asymmetric unit. Selenomethionine-labeled protein offers 40 selenium atoms for use in phasing. Structures of cyanase with bound chloride or oxalate anions, inhibitors of the enzyme, allowed identification of the active site. CONCLUSIONS: The cyanase monomer is composed of two domains. The N-terminal domain shows structural similarity to the DNA-binding alpha-helix bundle motif. The C-terminal domain has an 'open fold' with no structural homology to other proteins. The subunits of cyanase are arranged in a novel manner both at the dimer and decamer level. The dimer structure reveals the C-terminal domains to be intertwined, and the decamer is formed by a pentamer of these dimers. The active site of the enzyme is located between dimers and is comprised of residues from four adjacent subunits of the homodecamer. The structural data allow a conceivable reaction mechanism to be proposed.

-	~~==Function==~~	+	Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site.,Walsh MA, Otwinowski Z, Perrakis A, Anderson PM, Joachimiak A Structure. 2000 May 15;8(5):505-14. PMID:10801492<ref>PMID:10801492</ref>
-	~~[[http://www.uniprot.org/uniprot/CYNS_ECOLI CYNS_ECOLI]] Catalyzes the reaction~~ of ~~cyanate with bicarbonate to produce ammonia~~ and ~~carbon dioxide~~.	+

-	~~==About this Structure==~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[1dw9]] is~~ a ~~10 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Escherichia_coli Escherichia coli]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA].~~	+	</div>
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	~~<ref group="xtra">PMID:010801492</ref>~~<references ~~group="xtra"~~/><~~references~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Cyanase]]		[[Category: Cyanase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

OCA at 06:40, 10 April 2014

OCA — Thu, 10 Apr 2014 06:40:33 GMT

←Older revision		Revision as of 06:40, 10 April 2014
Line 1:		Line 1:
-	[[Image:1dw9.png\|left\|200px]]
-
-	<!--
-	The line below this paragraph, containing "STRUCTURE_1dw9", 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_1dw9\| PDB=1dw9 \| SCENE= }}		{{STRUCTURE_1dw9\| PDB=1dw9 \| SCENE= }}
-
	===STRUCTURE OF CYANASE REVEALS THAT A NOVEL DIMERIC AND DECAMERIC ARRANGEMENT OF SUBUNITS IS REQUIRED FOR FORMATION OF THE ENZYME ACTIVE SITE===		===STRUCTURE OF CYANASE REVEALS THAT A NOVEL DIMERIC AND DECAMERIC ARRANGEMENT OF SUBUNITS IS REQUIRED FOR FORMATION OF THE ENZYME ACTIVE SITE===
		+	{{ABSTRACT_PUBMED_10801492}}

-		+	==Function==
-	~~<!--~~	+	[[http://www.uniprot.org/uniprot/CYNS_ECOLI CYNS_ECOLI]] Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide.
-	~~The line below this paragraph, {{ABSTRACT_PUBMED_10801492}}, adds the Publication Abstract to the page~~	+
-	~~(as it appears on PubMed at~~ http://www.~~pubmed~~.~~gov), where 10801492 is~~ the ~~PubMed ID number~~.	+
-	~~-->~~	+
-	~~{{ABSTRACT_PUBMED_10801492}}~~	+

	==About this Structure==		==About this Structure==
Line 22:		Line 10:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:010801492</ref><~~ref~~ group="xtra"~~>PMID:002822670<~~/~~ref><ref group="xtra">PMID:003518792</ref><ref group="xtra">PMID:003651424</ref><ref group="xtra">PMID:006994799</ref~~><references ~~group="xtra"~~/>	+	<ref group="xtra">PMID:010801492</ref><references group="xtra"/><references/>
	[[Category: Cyanase]]		[[Category: Cyanase]]
	[[Category: Escherichia coli]]		[[Category: Escherichia coli]]

←Older revision		Revision as of 09:49, 26 May 2021
Line 3:		Line 3:
	<StructureSection load='1dw9' size='340' side='right'caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>		<StructureSection load='1dw9' size='340' side='right'caption='[[1dw9]], [[Resolution\|resolution]] 1.65Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1dw9]] is a 10 chain structure with sequence from [https://en.wikipedia.org/wiki/"bacillus_coli"_migula_1895 "bacillus coli" migula 1895]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DW9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DW9 FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>		<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1dwk\|1dwk]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1dwk\|1dwk]]</div></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cyanase Cyanase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.104 4.2.1.104] </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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [~~http~~://pdbe.org/1dw9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw9 ProSAT], [~~http~~://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</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=1dw9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dw9 OCA], [https://pdbe.org/1dw9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dw9 RCSB], [https://www.ebi.ac.uk/pdbsum/1dw9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dw9 ProSAT], [https://www.topsan.org/Proteins/MCSG/1dw9 TOPSAN]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[[~~http~~://www.uniprot.org/uniprot/CYNS_ECOLI CYNS_ECOLI]] Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide.	+	[[https://www.uniprot.org/uniprot/CYNS_ECOLI CYNS_ECOLI]] Catalyzes the reaction of cyanate with bicarbonate to produce ammonia and carbon dioxide.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]