1v1a - Revision history

OCA at 06:36, 1 May 2024

2024-05-01T06:36:10Z

←Older revision		Revision as of 06:36, 1 May 2024
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	<StructureSection load='1v1a' size='340' side='right'caption='[[1v1a]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1v1a' size='340' side='right'caption='[[1v1a]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1v1a]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Thet8 Thet8~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1V1A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1v1a]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V1A FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=ADP:ADENOSINE~~-~~5-DIPHOSPHATE'>ADP</scene>~~, ~~<scene name='pdbligand=KDG:~~2~~-KETO-3-DEOXYGLUCONATE'>KDG</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]] 2.1Å</td></tr>
-	<tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat"><~~div style~~='~~overflow~~: ~~auto; max~~-~~height: 3em;~~'>~~[[1j5v\|1j5v]]~~, ~~[[1v19\|1v19]], [[1v1b\|1v1b]]~~</~~div~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></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=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [~~http~~://pdbe.org/1v1a PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1v1a ProSAT], [~~http~~://www.topsan.org/Proteins/RSGI/1v1a 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=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [https://pdbe.org/1v1a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [https://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v1a ProSAT], [https://www.topsan.org/Proteins/RSGI/1v1a TOPSAN]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/KDGK_THET8 KDGK_THET8] Involved in the degradation of glucose via the semi-phosphorylative Entner-Doudoroff pathway. Catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to produce 2-keto-3-deoxy-6-phosphogluconate (KDPG).<ref>PMID:15210349</ref>
	== 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=1v1a 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=1v1a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The genome sequence of Thermus thermophilus HB8 contains an open reading frame that has a 30% identity to Escherichia coli KDGK. The KDGK activity of T.thermophilus protein (TtKDGK) has been confirmed, and its crystal structure has been determined by the molecular replacement method and refined with two crystal forms to 2.3 angstroms and 3.2 angstroms, respectively. The enzyme is a hexamer organized as a trimer of dimers. Each subunit is composed of two domains, a larger alpha/beta domain and a smaller beta-sheet domain, similar to that of ribokinase and adenosine kinase, members of the PfkB family of carbohydrate kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was determined and refined at 2.1 angstroms. The bound KDG was observed predominantly as an open chain structure. The positioning of ligands and the conservation of important catalytic residues suggest that the reaction mechanism is likely to be similar to that of other members of the PfkB family, including ribokinase. In particular, the Asp251 is postulated to have a role in transferring the gamma-phosphate of ATP to the 5'-hydroxyl group of KDG.
-
-	Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.,Ohshima N, Inagaki E, Yasuike K, Takio K, Tahirov TH J Mol Biol. 2004 Jul 9;340(3):477-89. PMID:15210349<ref>PMID:15210349</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1v1a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Thet8~~]]	+	[[Category: Thermus thermophilus HB8]]
-	[[Category: Inagaki, E]]	+	[[Category: Inagaki E]]
-	[[Category: Tahirov~~, T H]]~~	+	[[Category: Tahirov TH]]
-	~~[[Category: 2-keto-3-deoxygluconate kinase]]~~	+
-	~~[[Category: Atp]]~~	+
-	~~[[Category: Structural genomic]]~~	+
-	~~[[Category: Rsgi]]~~	+
-	~~[[Category: Thermus thermophilus]]~~	+
-	~~[[Category: Transferase~~]]	+

OCA at 07:31, 30 December 2020

2020-12-30T07:31:09Z

←Older revision		Revision as of 07:31, 30 December 2020
Line 1:		Line 1:

	==2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP==		==2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP==
-	<StructureSection load='1v1a' size='340' side='right' caption='[[1v1a]], [[Resolution\|resolution]] 2.10Å' scene=''>	+	<StructureSection load='1v1a' size='340' side='right'caption='[[1v1a]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1v1a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1V1A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1v1a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1V1A FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>
-	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j5v\|1j5v]], [[1v19\|1v19]], [[1v1b\|1v1b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1j5v\|1j5v]], [[1v19\|1v19]], [[1v1b\|1v1b]]</div></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=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [http://pdbe.org/1v1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [http://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v1a ProSAT], [http://www.topsan.org/Proteins/RSGI/1v1a 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=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [http://pdbe.org/1v1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [http://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v1a ProSAT], [http://www.topsan.org/Proteins/RSGI/1v1a TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 31:		Line 31:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: Thet8]]		[[Category: Thet8]]
	[[Category: Inagaki, E]]		[[Category: Inagaki, E]]

OCA at 07:49, 24 October 2018

2018-10-24T07:49:32Z

←Older revision		Revision as of 07:49, 24 October 2018
Line 12:		Line 12:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v1/1v1a_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v1/1v1a_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 35:		Line 35:
	[[Category: Tahirov, T H]]		[[Category: Tahirov, T H]]
	[[Category: 2-keto-3-deoxygluconate kinase]]		[[Category: 2-keto-3-deoxygluconate kinase]]
		+	[[Category: Atp]]
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 17:33, 18 January 2017

2017-01-18T17:33:33Z

←Older revision		Revision as of 17:33, 18 January 2017
Line 1:		Line 1:
		+
	==2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP==		==2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP==
	<StructureSection load='1v1a' size='340' side='right' caption='[[1v1a]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1v1a' size='340' side='right' caption='[[1v1a]], [[Resolution\|resolution]] 2.10Å' scene=''>
Line 5:		Line 6:
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j5v\|1j5v]], [[1v19\|1v19]], [[1v1b\|1v1b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j5v\|1j5v]], [[1v19\|1v19]], [[1v1b\|1v1b]]</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=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [http://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [http://www.topsan.org/Proteins/RSGI/1v1a 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=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [http://pdbe.org/1v1a PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [http://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1v1a ProSAT], [http://www.topsan.org/Proteins/RSGI/1v1a TOPSAN]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
Line 15:		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=1v1a ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 25:		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 1v1a" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>

OCA at 07:04, 15 April 2015

2015-04-15T07:04:10Z

←Older revision		Revision as of 07:04, 15 April 2015
Line 2:		Line 2:
	<StructureSection load='1v1a' size='340' side='right' caption='[[1v1a]], [[Resolution\|resolution]] 2.10Å' scene=''>		<StructureSection load='1v1a' size='340' side='right' caption='[[1v1a]], [[Resolution\|resolution]] 2.10Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1v1a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Thermus_thermophilus Thermus thermophilus~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V1A FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1v1a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thet8 Thet8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V1A FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>
	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j5v\|1j5v]], [[1v19\|1v19]], [[1v1b\|1v1b]]</td></tr>		<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j5v\|1j5v]], [[1v19\|1v19]], [[1v1b\|1v1b]]</td></tr>
Line 29:		Line 29:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Thermus thermophilus~~]]	+	[[Category: Thet8]]
	[[Category: Inagaki, E]]		[[Category: Inagaki, E]]
	[[Category: Tahirov, T H]]		[[Category: Tahirov, T H]]
Line 35:		Line 35:
	[[Category: Structural genomic]]		[[Category: Structural genomic]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
		+	[[Category: Thermus thermophilus]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 12:44, 6 January 2015

2015-01-06T12:44:05Z

←Older revision		Revision as of 12:44, 6 January 2015
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1v1a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V1A FirstGlance]. <br>		<table><tr><td colspan='2'>[[1v1a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V1A FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene></td></tr>
-	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j5v\|1j5v]], [[1v19\|1v19]], [[1v1b\|1v1b]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j5v\|1j5v]], [[1v19\|1v19]], [[1v1b\|1v1b]]</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=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [http://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [http://www.topsan.org/Proteins/RSGI/1v1a 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=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [http://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [http://www.topsan.org/Proteins/RSGI/1v1a TOPSAN]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
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	</StructureSection>		</StructureSection>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
-	[[Category: Inagaki, E.]]	+	[[Category: Inagaki, E]]
-	[[Category: Tahirov, T H.]]	+	[[Category: Tahirov, T H]]
	[[Category: 2-keto-3-deoxygluconate kinase]]		[[Category: 2-keto-3-deoxygluconate kinase]]
-	[[Category: ~~Riken structural genomics/proteomics initiative~~]]	+	[[Category: Structural genomic]]
	[[Category: Rsgi]]		[[Category: Rsgi]]
-	[[Category: Structural genomic]]
-	[[Category: Thermus thermophilus]]
	[[Category: Transferase]]		[[Category: Transferase]]

OCA at 20:30, 29 September 2014

2014-09-29T20:30:36Z

←Older revision		Revision as of 20:30, 29 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1v1a.~~png~~\|~~left~~\|200px]]	+	==2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP==
		+	<StructureSection load='1v1a' size='340' side='right' caption='[[1v1a]], [[Resolution\|resolution]] 2.10Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1v1a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1V1A FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=KDG:2-KETO-3-DEOXYGLUCONATE'>KDG</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1j5v\|1j5v]], [[1v19\|1v19]], [[1v1b\|1v1b]]</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=1v1a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v1a OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1v1a RCSB], [http://www.ebi.ac.uk/pdbsum/1v1a PDBsum], [http://www.topsan.org/Proteins/RSGI/1v1a 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/v1/1v1a_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 ==
		+	2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The genome sequence of Thermus thermophilus HB8 contains an open reading frame that has a 30% identity to Escherichia coli KDGK. The KDGK activity of T.thermophilus protein (TtKDGK) has been confirmed, and its crystal structure has been determined by the molecular replacement method and refined with two crystal forms to 2.3 angstroms and 3.2 angstroms, respectively. The enzyme is a hexamer organized as a trimer of dimers. Each subunit is composed of two domains, a larger alpha/beta domain and a smaller beta-sheet domain, similar to that of ribokinase and adenosine kinase, members of the PfkB family of carbohydrate kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was determined and refined at 2.1 angstroms. The bound KDG was observed predominantly as an open chain structure. The positioning of ligands and the conservation of important catalytic residues suggest that the reaction mechanism is likely to be similar to that of other members of the PfkB family, including ribokinase. In particular, the Asp251 is postulated to have a role in transferring the gamma-phosphate of ATP to the 5'-hydroxyl group of KDG.

-	~~{{STRUCTURE_1v1a\| PDB=1v1a \| SCENE= }}~~	+	Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate.,Ohshima N, Inagaki E, Yasuike K, Takio K, Tahirov TH J Mol Biol. 2004 Jul 9;340(3):477-89. PMID:15210349<ref>PMID:15210349</ref>

-	~~===2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_15210349}}~~	+	== References ==
-		+	<references/>
-	~~==About this Structure==~~	+	__TOC__
-	~~[[1v1a]] is~~ a ~~2 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Thermus_thermophilus Thermus thermophilus]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA].~~	+	</StructureSection>
-		+
-	==~~Reference~~==	+
-	<~~ref group="xtra">PMID:015210349<~~/~~ref~~><~~ref group="xtra">PMID:015039578</ref><references group="xtra"~~/>	+
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Inagaki, E.]]		[[Category: Inagaki, E.]]

OCA at 09:52, 16 January 2013

2013-01-16T09:52:12Z

←Older revision		Revision as of 09:52, 16 January 2013
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	[[Image:1v1a.png\|left\|200px]]		[[Image:1v1a.png\|left\|200px]]

-	<!--
-	The line below this paragraph, containing "STRUCTURE_1v1a", 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_1v1a\| PDB=1v1a \| SCENE= }}		{{STRUCTURE_1v1a\| PDB=1v1a \| SCENE= }}

	===2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP===		===2-KETO-3-DEOXYGLUCONATE KINASE FROM THERMUS THERMOPHILUS WITH BOUND 2-KETO-3-DEOXYGLUCONATE AND ADP===

-
-	<!--
-	The line below this paragraph, {{ABSTRACT_PUBMED_15210349}}, adds the Publication Abstract to the page
-	(as it appears on PubMed at http://www.pubmed.gov), where 15210349 is the PubMed ID number.
-	-->
	{{ABSTRACT_PUBMED_15210349}}		{{ABSTRACT_PUBMED_15210349}}

Line 22:		Line 11:

	==Reference==		==Reference==
-	<ref group="xtra">PMID:~~15210349~~</ref><ref group="xtra">PMID:~~15039578~~</ref><references group="xtra"/>	+	<ref group="xtra">PMID:015210349</ref><ref group="xtra">PMID:015039578</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Inagaki, E.]]		[[Category: Inagaki, E.]]
	[[Category: Tahirov, T H.]]		[[Category: Tahirov, T H.]]
	[[Category: 2-keto-3-deoxygluconate kinase]]		[[Category: 2-keto-3-deoxygluconate kinase]]
-	[[Category: Atp]]
	[[Category: Riken structural genomics/proteomics initiative]]		[[Category: Riken structural genomics/proteomics initiative]]
	[[Category: Rsgi]]		[[Category: Rsgi]]

OCA: Protected "1v1a" [edit=sysop:move=sysop]

2011-03-14T18:36:57Z

Protected "1v1a" [edit=sysop:move=sysop]

←Older revision

Revision as of 18:36, 14 March 2011

OCA at 18:36, 14 March 2011

2011-03-14T18:36:55Z

←Older revision		Revision as of 18:36, 14 March 2011
Line 1:		Line 1:
-	{{Seed}}
	[[Image:1v1a.png\|left\|200px]]		[[Image:1v1a.png\|left\|200px]]

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	==About this Structure==		==About this Structure==
-	~~1V1A~~ is a 2 ~~chains~~ structure ~~of sequences~~ from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA].	+	[[1v1a]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V1A OCA].

	==Reference==		==Reference==
-	<ref group="xtra">PMID:15210349</ref><references group="xtra"/>	+	<ref group="xtra">PMID:15210349</ref><ref group="xtra">PMID:15039578</ref><references group="xtra"/>
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Inagaki, E.]]		[[Category: Inagaki, E.]]
-	[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
	[[Category: Tahirov, T H.]]		[[Category: Tahirov, T H.]]
	[[Category: 2-keto-3-deoxygluconate kinase]]		[[Category: 2-keto-3-deoxygluconate kinase]]
Line 35:		Line 33:
	[[Category: Thermus thermophilus]]		[[Category: Thermus thermophilus]]
	[[Category: Transferase]]		[[Category: Transferase]]
-
-	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 07:28:23 2009''