1bux - Revision history

OCA at 06:39, 7 February 2024

OCA — Wed, 07 Feb 2024 06:39:11 GMT

←Older revision		Revision as of 06:39, 7 February 2024
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	<StructureSection load='1bux' size='340' side='right'caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1bux' size='340' side='right'caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/~~Atcc_11735 Atcc 11735~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BUX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BUX FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=PPS:3~~-~~PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</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]] 2.8Å</td></tr>
-	<tr id='~~activity~~'><td class="sblockLbl"><b>~~Activity~~:</b></td><td class="sblockDat"><~~span class~~='~~plainlinks'>[https~~:~~//en.wikipedia.org/wiki/Nucleoside~~-~~diphosphate_kinase Nucleoside~~-~~diphosphate kinase], with EC number [https://www.brenda~~-~~enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6]~~ </~~span~~></td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [https://pdbe.org/1bux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [https://www.ebi.ac.uk/pdbsum/1bux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bux ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [https://pdbe.org/1bux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [https://www.ebi.ac.uk/pdbsum/1bux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bux ProSAT]</span></td></tr>
	</table>		</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
	== 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=1bux 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=1bux ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Nucleoside diphosphate (NDP) kinase catalyzes the phosphorylation of ribo- and deoxyribonucleosides diphosphates into triphosphates. NDP kinase is also involved in malignant tumors and was shown to activate in vitro transcription of the c-myc oncogene by binding to its NHE sequence. The structure of the complex of NDP kinase with bound ADP shows that the nucleotide adopts a different conformation from that observed in other phosphokinases with an internal H bond between the 3'-OH and the beta-O made free by the phosphate transfer. We use intrinsic protein fluorescence to investigate the inhibitory and binding potential of nucleotide analogues phosphorylated in 3'-OH position of the ribose to both wild type and F64W mutant NDP kinase from Dictyostelium discoideum. Due to their 3'-phosphate, 5'-phosphoadenosine 3'-phosphate (PAP) and adenosine 3'-phosphate 5'-phosphosulfate (PAPS) can be regarded as structural analogues of enzyme-bound ADP. The KD of PAPS (10 microM) is three times lower than the KD of ADP. PAPS also acts as a competitive inhibitor toward natural substrates during catalysis, with a KI in agreement with binding data. The crystal structure of the binary complex between Dictyostelium NDP kinase and PAPS was solved at 2.8-A resolution. It shows a new mode of nucleotide binding at the active site with the 3'-phosphate of PAPS located near the catalytic histidine, at the same position as the gamma-phosphate in the transition state. The sulfate group is directed toward the protein surface. PAPS will be useful for the design of high affinity drugs targeted to NDP kinases.
-
-	3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity.,Schneider B, Xu YW, Janin J, Veron M, Deville-Bonne D J Biol Chem. 1998 Oct 30;273(44):28773-8. PMID:9786875<ref>PMID:9786875</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1bux" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Nucleoside diphosphate kinase 3D structures\|Nucleoside diphosphate kinase 3D structures]]		*[[Nucleoside diphosphate kinase 3D structures\|Nucleoside diphosphate kinase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Atcc 11735~~]]	+	[[Category: Dictyostelium discoideum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	~~[[Category: Nucleoside-diphosphate kinase]]~~	+	[[Category: Deville-Bonne D]]
-	[[Category: Deville-Bonne, D]]	+	[[Category: Janin J]]
-	[[Category: Janin, J]]	+	[[Category: Schneider B]]
-	[[Category: Schneider, B]]	+	[[Category: Veron M]]
-	[[Category: Veron, M]]	+	[[Category: Xu Y]]
-	[[Category: Xu, Y]]	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Pap]]~~	+
-	~~[[Category: Phosphotransferase~~]]	+

OCA at 10:30, 14 July 2021

OCA — Wed, 14 Jul 2021 10:30:04 GMT

←Older revision		Revision as of 10:30, 14 July 2021
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	<StructureSection load='1bux' size='340' side='right'caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1bux' size='340' side='right'caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1BUX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BUX FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene></td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [~~http~~://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [~~http~~://pdbe.org/1bux PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1bux PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1bux ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [https://pdbe.org/1bux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [https://www.ebi.ac.uk/pdbsum/1bux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bux ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	==See Also==		==See Also==
-	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]	+	*[[Nucleoside diphosphate kinase 3D structures\|Nucleoside diphosphate kinase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 06:58, 10 October 2019

OCA — Thu, 10 Oct 2019 06:58:26 GMT

←Older revision		Revision as of 06:58, 10 October 2019
Line 1:		Line 1:

	==3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==		==3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==
-	<StructureSection load='1bux' size='340' side='right' caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>	+	<StructureSection load='1bux' size='340' side='right'caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUX FirstGlance]. <br>
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/bu/1bux_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bu/1bux_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 27:		Line 27:
	</div>		</div>
	<div class="pdbe-citations 1bux" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1bux" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Atcc 11735]]		[[Category: Atcc 11735]]
		+	[[Category: Large Structures]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Deville-Bonne, D]]		[[Category: Deville-Bonne, D]]

OCA at 08:17, 29 November 2017

OCA — Wed, 29 Nov 2017 08:17:51 GMT

←Older revision		Revision as of 08:17, 29 November 2017
Line 1:		Line 1:
		+
	==3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==		==3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==
	<StructureSection load='1bux' size='340' side='right' caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1bux' size='340' side='right' caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>
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	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [http://pdbe.org/1bux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [http://www.ebi.ac.uk/pdbsum/1bux PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [http://pdbe.org/1bux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [http://www.ebi.ac.uk/pdbsum/1bux PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1bux ProSAT]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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	</div>		</div>
	<div class="pdbe-citations 1bux" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1bux" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 16:54, 9 February 2016

OCA — Tue, 09 Feb 2016 16:54:48 GMT

←Older revision		Revision as of 16:54, 9 February 2016
Line 15:		Line 15:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
-	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1bux ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:16, 11 September 2015

OCA — Fri, 11 Sep 2015 00:16:40 GMT

←Older revision		Revision as of 00:16, 11 September 2015
Line 2:		Line 2:
	<StructureSection load='1bux' size='340' side='right' caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>		<StructureSection load='1bux' size='340' side='right' caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Dictyostelium_discoideum Dictyostelium discoideum~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUX FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUX FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene></td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [http://www.ebi.ac.uk/pdbsum/1bux PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [http://pdbe.org/1bux PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [http://www.ebi.ac.uk/pdbsum/1bux PDBsum]</span></td></tr>
	</table>		</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
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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 1bux" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
Line 32:		Line 33:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Dictyostelium discoideum~~]]	+	[[Category: Atcc 11735]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
	[[Category: Deville-Bonne, D]]		[[Category: Deville-Bonne, D]]

OCA at 10:51, 22 December 2014

OCA — Mon, 22 Dec 2014 10:51:36 GMT

←Older revision		Revision as of 10:51, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUX FirstGlance]. <br>		<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUX FirstGlance]. <br>
-	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene><br>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene></td></tr>
-	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>	+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [http://www.ebi.ac.uk/pdbsum/1bux PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [http://www.ebi.ac.uk/pdbsum/1bux PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 34:		Line 34:
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]
-	[[Category: Deville-Bonne, D.]]	+	[[Category: Deville-Bonne, D]]
-	[[Category: Janin, J.]]	+	[[Category: Janin, J]]
-	[[Category: Schneider, B.]]	+	[[Category: Schneider, B]]
-	[[Category: Veron, M.]]	+	[[Category: Veron, M]]
-	[[Category: Xu, Y.]]	+	[[Category: Xu, Y]]
	[[Category: Inhibitor]]		[[Category: Inhibitor]]
	[[Category: Pap]]		[[Category: Pap]]
	[[Category: Phosphotransferase]]		[[Category: Phosphotransferase]]

OCA at 09:47, 13 August 2014

OCA — Wed, 13 Aug 2014 09:47:06 GMT

←Older revision		Revision as of 09:47, 13 August 2014
Line 1:		Line 1:
-	[[~~Image~~:1bux.~~png\|left~~\|200px]]	+	==3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==
		+	<StructureSection load='1bux' size='340' side='right' caption='[[1bux]], [[Resolution\|resolution]] 2.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1bux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1BUX FirstGlance]. <br>
		+	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene><br>
		+	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [http://www.ebi.ac.uk/pdbsum/1bux PDBsum]</span></td></tr>
		+	<table>
		+	== Evolutionary Conservation ==
		+	[[Image:Consurf_key_small.gif\|200px\|right]]
		+	Check<jmol>
		+	<jmolCheckbox>
		+	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bu/1bux_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 ==
		+	Nucleoside diphosphate (NDP) kinase catalyzes the phosphorylation of ribo- and deoxyribonucleosides diphosphates into triphosphates. NDP kinase is also involved in malignant tumors and was shown to activate in vitro transcription of the c-myc oncogene by binding to its NHE sequence. The structure of the complex of NDP kinase with bound ADP shows that the nucleotide adopts a different conformation from that observed in other phosphokinases with an internal H bond between the 3'-OH and the beta-O made free by the phosphate transfer. We use intrinsic protein fluorescence to investigate the inhibitory and binding potential of nucleotide analogues phosphorylated in 3'-OH position of the ribose to both wild type and F64W mutant NDP kinase from Dictyostelium discoideum. Due to their 3'-phosphate, 5'-phosphoadenosine 3'-phosphate (PAP) and adenosine 3'-phosphate 5'-phosphosulfate (PAPS) can be regarded as structural analogues of enzyme-bound ADP. The KD of PAPS (10 microM) is three times lower than the KD of ADP. PAPS also acts as a competitive inhibitor toward natural substrates during catalysis, with a KI in agreement with binding data. The crystal structure of the binary complex between Dictyostelium NDP kinase and PAPS was solved at 2.8-A resolution. It shows a new mode of nucleotide binding at the active site with the 3'-phosphate of PAPS located near the catalytic histidine, at the same position as the gamma-phosphate in the transition state. The sulfate group is directed toward the protein surface. PAPS will be useful for the design of high affinity drugs targeted to NDP kinases.

-	~~{{STRUCTURE_1bux\| PDB=1bux \| SCENE= }}~~	+	3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity.,Schneider B, Xu YW, Janin J, Veron M, Deville-Bonne D J Biol Chem. 1998 Oct 30;273(44):28773-8. PMID:9786875<ref>PMID:9786875</ref>

-	~~===3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~{{ABSTRACT_PUBMED_9786875}}~~	+
-		+
-	~~==About this Structure==~~	+
-	~~[[1bux]] is~~ a ~~3 chain structure with sequence from [http://en~~.~~wikipedia~~.~~org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]~~. ~~Full crystallographic information is available from [http:~~/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA].~~	+

	==See Also==		==See Also==
	*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]		*[[Nucleoside diphosphate kinase\|Nucleoside diphosphate kinase]]
-		+	== References ==
-	==~~Reference~~==	+	<references/>
-	<~~ref group="xtra">PMID:009786875<~~/~~ref~~><~~references group="xtra"~~/>	+	__TOC__
		+	</StructureSection>
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
	[[Category: Nucleoside-diphosphate kinase]]		[[Category: Nucleoside-diphosphate kinase]]

OCA at 14:31, 20 October 2012

OCA — Sat, 20 Oct 2012 14:31:26 GMT

←Older revision		Revision as of 14:31, 20 October 2012
Line 8:		Line 8:

	==About this Structure==		==About this Structure==
-	[[1bux]] is a 3 chain structure ~~of [[Nucleoside diphosphate kinase]]~~ with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA].	+	[[1bux]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BUX OCA].

	==See Also==		==See Also==

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

OCA — Thu, 26 Jul 2012 15:25:12 GMT

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

←Older revision

Revision as of 15:25, 26 July 2012