1wq7 - Revision history

OCA at 13:33, 13 March 2024

OCA — Wed, 13 Mar 2024 13:33:31 GMT

←Older revision		Revision as of 13:33, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='1wq7' size='340' side='right'caption='[[1wq7]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1wq7' size='340' side='right'caption='[[1wq7]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii~~ Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"~~><div style='overflow: auto; max-height: 3em;'>[[1wnl\|1wnl]], [[1wpy\|1wpy]]</div></td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 1.6Å</td></tr>
-	~~<tr~~ id~~='gene'><td class~~="~~sblockLbl~~">~~<b>~~[[~~Gene~~\|~~Gene:~~]]~~</b></td><td class="sblockDat">birA ([http://www~~.~~ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info~~&~~srchmode=5&id=70601 Pyrococcus horikoshii])</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=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [https://pdbe.org/1wq7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [https://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wq7 ProSAT], [https://www.topsan.org/Proteins/RSGI/1wq7 TOPSAN]</span></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </span></td></tr>	+
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [~~http~~://pdbe.org/1wq7 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1wq7 ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1wq7 TOPSAN]</span></td></tr>	+
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/O57883_PYRHO O57883_PYRHO]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 19:		Line 19:
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1wq7 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=1wq7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Biotin protein ligase (EC 6.3.4.15) catalyses the synthesis of an activated form of biotin, biotinyl-5'-AMP, from substrates biotin and ATP followed by biotinylation of the biotin carboxyl carrier protein subunit of acetyl-CoA carboxylase. The three-dimensional structure of biotin protein ligase from Pyrococcus horikoshii OT3 has been determined by X-ray diffraction at 1.6A resolution. The structure reveals a homodimer as the functional unit. Each subunit contains two domains, a larger N-terminal catalytic domain and a smaller C-terminal domain. The structural feature of the active site has been studied by determination of the crystal structures of complexes of the enzyme with biotin, ADP and the reaction intermediate biotinyl-5'-AMP at atomic resolution. This is the first report of the liganded structures of biotin protein ligase with nucleotide and biotinyl-5'-AMP. The structures of the unliganded and the liganded forms are isomorphous except for an ordering of the active site loop upon ligand binding. Catalytic binding sites are suitably arranged to minimize the conformational changes required during the reaction, as the pockets for biotin and nucleotide are located spatially adjacent to each other in a cleft of the catalytic domain and the pocket for biotinyl-5'-AMP binding mimics the combination of those of the substrates. The exact locations of the ligands and the active site residues allow us to propose a general scheme for the first step of the reaction carried out by biotin protein ligase in which the positively charged epsilon-amino group of Lys111 facilitates the nucleophilic attack on the ATP alpha-phosphate group by the biotin carboxyl oxygen atom and stabilizes the negatively charged intermediates.
-
-	Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation.,Bagautdinov B, Kuroishi C, Sugahara M, Kunishima N J Mol Biol. 2005 Oct 21;353(2):322-33. PMID:16169557<ref>PMID:16169557</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1wq7" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Biotin Protein Ligase 3D structures\|Biotin Protein Ligase 3D structures]]		*[[Biotin Protein Ligase 3D structures\|Biotin Protein Ligase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Pyrococcus horikoshii]]	+	[[Category: Pyrococcus horikoshii OT3]]
-	[[Category: Bagautdinov, B]]	+	[[Category: Bagautdinov B]]
-	[[Category: Kunishima, N]]	+	[[Category: Kunishima N]]
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Biotin biosynthesis]]~~	+
-	~~[[Category: Dimer]]~~	+
-	~~[[Category: Ligase]]~~	+
-	~~[[Category: Rsgi~~]]	+

OCA at 09:26, 6 January 2021

OCA — Wed, 06 Jan 2021 09:26:07 GMT

←Older revision		Revision as of 09:26, 6 January 2021
Line 1:		Line 1:

	==Crystal Structure Of Biotin-(Acetyl-CoA-Carboxylase) ligase From Pyrococcus Horikoshii Ot3==		==Crystal Structure Of Biotin-(Acetyl-CoA-Carboxylase) ligase From Pyrococcus Horikoshii Ot3==
-	<StructureSection load='1wq7' size='340' side='right' caption='[[1wq7]], [[Resolution\|resolution]] 1.60Å' scene=''>	+	<StructureSection load='1wq7' size='340' side='right'caption='[[1wq7]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>
-	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnl\|1wnl]], [[1wpy\|1wpy]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1wnl\|1wnl]], [[1wpy\|1wpy]]</div></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </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=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [http://pdbe.org/1wq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wq7 ProSAT], [http://www.topsan.org/Proteins/RSGI/1wq7 TOPSAN]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [http://pdbe.org/1wq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wq7 ProSAT], [http://www.topsan.org/Proteins/RSGI/1wq7 TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 30:		Line 30:

	==See Also==		==See Also==
-	*[[Biotin Protein Ligase\|Biotin Protein Ligase]]	+	*[[Biotin Protein Ligase 3D structures\|Biotin Protein Ligase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Bagautdinov, B]]		[[Category: Bagautdinov, B]]

OCA at 08:01, 25 July 2018

OCA — Wed, 25 Jul 2018 08:01:09 GMT

←Older revision		Revision as of 08:01, 25 July 2018
Line 13:		Line 13:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wq/1wq7_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wq/1wq7_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 28:		Line 28:
	</div>		</div>
	<div class="pdbe-citations 1wq7" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1wq7" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Biotin Protein Ligase\|Biotin Protein Ligase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:21, 18 October 2016

OCA — Tue, 18 Oct 2016 07:21:08 GMT

←Older revision		Revision as of 07:21, 18 October 2016
Line 1:		Line 1:
		+
	==Crystal Structure Of Biotin-(Acetyl-CoA-Carboxylase) ligase From Pyrococcus Horikoshii Ot3==		==Crystal Structure Of Biotin-(Acetyl-CoA-Carboxylase) ligase From Pyrococcus Horikoshii Ot3==
	<StructureSection load='1wq7' size='340' side='right' caption='[[1wq7]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1wq7' size='340' side='right' caption='[[1wq7]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrho Pyrho~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnl\|1wnl]], [[1wpy\|1wpy]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnl\|1wnl]], [[1wpy\|1wpy]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 ~~PYRHO~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </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=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [http://pdbe.org/1wq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [http://www.topsan.org/Proteins/RSGI/1wq7 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=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [http://pdbe.org/1wq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wq7 ProSAT], [http://www.topsan.org/Proteins/RSGI/1wq7 TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 32:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrho~~]]	+	[[Category: Pyrococcus horikoshii]]
	[[Category: Bagautdinov, B]]		[[Category: Bagautdinov, B]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]

OCA at 02:18, 7 February 2016

OCA — Sun, 07 Feb 2016 02:18:40 GMT

←Older revision		Revision as of 02:18, 7 February 2016
Line 16:		Line 16:
	<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=1wq7 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 20:44, 9 September 2015

OCA — Wed, 09 Sep 2015 20:44:23 GMT

←Older revision		Revision as of 20:44, 9 September 2015
Line 2:		Line 2:
	<StructureSection load='1wq7' size='340' side='right' caption='[[1wq7]], [[Resolution\|resolution]] 1.60Å' scene=''>		<StructureSection load='1wq7' size='340' side='right' caption='[[1wq7]], [[Resolution\|resolution]] 1.60Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Pyrococcus_horikoshii Pyrococcus horikoshii~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrho Pyrho]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnl\|1wnl]], [[1wpy\|1wpy]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnl\|1wnl]], [[1wpy\|1wpy]]</td></tr>
-	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=~~53953 Pyrococcus horikoshii~~])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 PYRHO])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </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=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [http://www.topsan.org/Proteins/RSGI/1wq7 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=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [http://pdbe.org/1wq7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [http://www.topsan.org/Proteins/RSGI/1wq7 TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 26:		Line 26:
	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 1wq7" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Pyrococcus horikoshii~~]]	+	[[Category: Pyrho]]
	[[Category: Bagautdinov, B]]		[[Category: Bagautdinov, B]]
	[[Category: Kunishima, N]]		[[Category: Kunishima, N]]

OCA at 12:33, 6 January 2015

OCA — Tue, 06 Jan 2015 12:33:39 GMT

←Older revision		Revision as of 12:33, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnl\|1wnl]], [[1wpy\|1wpy]]</td></tr>	+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnl\|1wnl]], [[1wpy\|1wpy]]</td></tr>
-	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>	+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </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=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [http://www.topsan.org/Proteins/RSGI/1wq7 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=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [http://www.topsan.org/Proteins/RSGI/1wq7 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 31:		Line 31:
	</StructureSection>		</StructureSection>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
-	[[Category: Bagautdinov, B.]]	+	[[Category: Bagautdinov, B]]
-	[[Category: Kunishima, N.]]	+	[[Category: Kunishima, N]]
-	[[Category: ~~RSGI, RIKEN~~ Structural ~~Genomics/Proteomics Initiative.~~]]	+	[[Category: Structural genomic]]
	[[Category: Biotin biosynthesis]]		[[Category: Biotin biosynthesis]]
	[[Category: Dimer]]		[[Category: Dimer]]
	[[Category: Ligase]]		[[Category: Ligase]]
-	[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]

OCA at 18:28, 29 September 2014

OCA — Mon, 29 Sep 2014 18:28:38 GMT

←Older revision		Revision as of 18:28, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1wq7.~~png~~\|~~left~~\|200px]]	+	==Crystal Structure Of Biotin-(Acetyl-CoA-Carboxylase) ligase From Pyrococcus Horikoshii Ot3==
		+	<StructureSection load='1wq7' size='340' side='right' caption='[[1wq7]], [[Resolution\|resolution]] 1.60Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WQ7 FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1wnl\|1wnl]], [[1wpy\|1wpy]]</td></tr>
		+	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">birA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=53953 Pyrococcus horikoshii])</td></tr>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Biotin--[acetyl-CoA-carboxylase]_ligase Biotin--[acetyl-CoA-carboxylase] ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.3.4.15 6.3.4.15] </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=1wq7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wq7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1wq7 RCSB], [http://www.ebi.ac.uk/pdbsum/1wq7 PDBsum], [http://www.topsan.org/Proteins/RSGI/1wq7 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/wq/1wq7_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 ==
		+	Biotin protein ligase (EC 6.3.4.15) catalyses the synthesis of an activated form of biotin, biotinyl-5'-AMP, from substrates biotin and ATP followed by biotinylation of the biotin carboxyl carrier protein subunit of acetyl-CoA carboxylase. The three-dimensional structure of biotin protein ligase from Pyrococcus horikoshii OT3 has been determined by X-ray diffraction at 1.6A resolution. The structure reveals a homodimer as the functional unit. Each subunit contains two domains, a larger N-terminal catalytic domain and a smaller C-terminal domain. The structural feature of the active site has been studied by determination of the crystal structures of complexes of the enzyme with biotin, ADP and the reaction intermediate biotinyl-5'-AMP at atomic resolution. This is the first report of the liganded structures of biotin protein ligase with nucleotide and biotinyl-5'-AMP. The structures of the unliganded and the liganded forms are isomorphous except for an ordering of the active site loop upon ligand binding. Catalytic binding sites are suitably arranged to minimize the conformational changes required during the reaction, as the pockets for biotin and nucleotide are located spatially adjacent to each other in a cleft of the catalytic domain and the pocket for biotinyl-5'-AMP binding mimics the combination of those of the substrates. The exact locations of the ligands and the active site residues allow us to propose a general scheme for the first step of the reaction carried out by biotin protein ligase in which the positively charged epsilon-amino group of Lys111 facilitates the nucleophilic attack on the ATP alpha-phosphate group by the biotin carboxyl oxygen atom and stabilizes the negatively charged intermediates.

-	~~{{STRUCTURE_1wq7\| PDB=1wq7 \| SCENE= }}~~	+	Crystal structures of biotin protein ligase from Pyrococcus horikoshii OT3 and its complexes: structural basis of biotin activation.,Bagautdinov B, Kuroishi C, Sugahara M, Kunishima N J Mol Biol. 2005 Oct 21;353(2):322-33. PMID:16169557<ref>PMID:16169557</ref>

-	~~===Crystal Structure Of Biotin-(Acetyl-CoA-Carboxylase) ligase~~ From ~~Pyrococcus Horikoshii Ot3===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_16169557}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1wq7]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:016169557<~~/~~ref~~><~~references group="xtra"~~/>	+
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Bagautdinov, B.]]		[[Category: Bagautdinov, B.]]

OCA: Protected "1wq7" [edit=sysop:move=sysop]

OCA — Sat, 05 Jan 2013 11:06:38 GMT

Protected "1wq7" [edit=sysop:move=sysop]

←Older revision

Revision as of 11:06, 5 January 2013

OCA at 11:06, 5 January 2013

OCA — Sat, 05 Jan 2013 11:06:34 GMT

←Older revision		Revision as of 11:06, 5 January 2013
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1wq7.png\|left\|200px]]		[[Image:1wq7.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1wq7", 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_1wq7\| PDB=1wq7 \| SCENE= }}		{{STRUCTURE_1wq7\| PDB=1wq7 \| SCENE= }}

	===Crystal Structure Of Biotin-(Acetyl-CoA-Carboxylase) ligase From Pyrococcus Horikoshii Ot3===		===Crystal Structure Of Biotin-(Acetyl-CoA-Carboxylase) ligase From Pyrococcus Horikoshii Ot3===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_16169557}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 16169557 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_16169557}}		{{ABSTRACT_PUBMED_16169557}}

	==About this Structure==		==About this Structure==
-	~~1WQ7~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA].	+	[[1wq7]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WQ7 OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~16169557~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:016169557</ref><references group="xtra"/>
	[[Category: Pyrococcus horikoshii]]		[[Category: Pyrococcus horikoshii]]
	[[Category: Bagautdinov, B.]]		[[Category: Bagautdinov, B.]]
Line 30:		Line 18:
	[[Category: Biotin biosynthesis]]		[[Category: Biotin biosynthesis]]
	[[Category: Dimer]]		[[Category: Dimer]]
		+	[[Category: Ligase]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
-	[[Category: X-ray diffraction]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 10:15:22 2009''