1uke - Revision history

OCA at 08:45, 14 February 2024

2024-02-14T08:45:30Z

← Older revision		Revision as of 08:45, 14 February 2024
Line 3:		Line 3:
	<StructureSection load='1uke' size='340' side='right'caption='[[1uke]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1uke' size='340' side='right'caption='[[1uke]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1uke]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Atcc_11735 Atcc 11735~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=1UKE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1uke]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UKE FirstGlance]. <br>
	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>~~, ~~<scene name='pdbligand=UP5:P1-(ADENOSINE-5-P5-(URIDINE-5)PENTAPHOSPHATE'>UP5</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]] 2.2Å</td></tr>
	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~44689 ATCC 11735])</td~~><~~/tr>~~		<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UP5:P1-(ADENOSINE-5-P5-(URIDINE-5)PENTAPHOSPHATE'>UP5</scene></td></tr>
	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14]~~ </~~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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [https://pdbe.org/1uke PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [https://www.ebi.ac.uk/pdbsum/1uke PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uke ProSAT]</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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [~~http~~://pdbe.org/1uke PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1uke PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1uke ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[~~[http~~://www.uniprot.org/uniprot/KCY_DICDI KCY_DICDI]] This UMP-CMP kinase uses preferentially ATP as phosphate donor and is specific for UMP and CMP.		[https://www.uniprot.org/uniprot/KCY_DICDI KCY_DICDI] This UMP-CMP kinase uses preferentially ATP as phosphate donor and is specific for UMP and CMP.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 21:		Line 20:
	</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=1uke 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=1uke ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	~~<div style="background-color:#fffaf0;">~~
	~~== Publication Abstract from PubMed ==~~
	The three-dimensional structure of the UMP/CMP kinase (UK) from the slime mold Dictyostelium discoideum complexed with the specific and asymmetric bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) has been determined at a resolution of 2.2 A. The structure of the enzyme, which has up to 41% sequence homology with known adenylate kinases (AK), represents a closed conformation with the flexible monophosphate binding domain (NMP site) being closed over the uridyl moiety of the dinucleotide. Two water molecules were found within hydrogen-bonding distance to the uracil base. The key residue for the positioning and stabilization of those water molecules appears to be asparagine 97, a residue that is highly specific for AK-homologous UMP kinases, but is almost invariably a glutamine in adenylate kinases. Other residues in this region are highly conserved among AK-related NMP kinases. The catalytic Mg2+ ion is coordinated with octahedral geometry to four water molecules and two oxygens of the phosphate chain of UP5A but has no direct interactions with the protein. The comparison of the geometry of the UKdicty.UP5A.Mg2+ complex with the previously reported structure of the UKyeast.ADP.ADP complex [Muller-Dieckmann & Schulz (1994) J. Mol. Biol. 236, 361-367] suggests that UP5A in our structure mimics an ADP.Mg.UDP biproduct inhibitor rather than an ATP. MG.UMP bisubstrate inhibitor.

	Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity.,Scheffzek K, Kliche W, Wiesmuller L, Reinstein J Biochemistry. 1996 Jul 30;35(30):9716-27. PMID:8703943<ref>PMID:8703943</ref>

	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~
	~~</div>~~
	~~<div class="pdbe-citations 1uke" style="background-color:#fffaf0;"></div>~~

	==See Also==		==See Also==
	*[[UMP/CMP kinase\|UMP/CMP kinase]]		*[[UMP/CMP kinase\|UMP/CMP kinase]]
	~~== References ==~~
	~~<references/>~~
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Atcc 11735~~]]		[[Category: Dictyostelium discoideum]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	~~[[Category: UMP/CMP kinase]]~~		[[Category: Kliche W]]
	[[Category: Kliche, W]]		[[Category: Reinstein J]]
	[[Category: Reinstein, J]]		[[Category: Scheffzek K]]
	[[Category: Scheffzek, K]]		[[Category: Wiesmueller L]]
	[[Category: Wiesmueller, L]]
	~~[[Category: Bisubstrate inhibitor]]~~
	~~[[Category: Nmp kinase]]~~
	~~[[Category: Nucleotide monophosphate kinase]]~~
	~~[[Category: Nucleotide specificity]]~~
	~~[[Category: Phosphoryl transfer~~]]

OCA at 07:29, 30 December 2020

2020-12-30T07:29:18Z

← Older revision		Revision as of 07:29, 30 December 2020
Line 1:		Line 1:

	==UMP/CMP KINASE FROM SLIME MOLD==		==UMP/CMP KINASE FROM SLIME MOLD==
	<StructureSection load='1uke' size='340' side='right' caption='[[1uke]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1uke' size='340' side='right'caption='[[1uke]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1uke]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1UKE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1uke]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1UKE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UP5:P1-(ADENOSINE-5-P5-(URIDINE-5)PENTAPHOSPHATE'>UP5</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UP5:P1-(ADENOSINE-5-P5-(URIDINE-5)PENTAPHOSPHATE'>UP5</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 ATCC 11735])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 ATCC 11735])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [http://pdbe.org/1uke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [http://www.ebi.ac.uk/pdbsum/1uke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1uke ProSAT]</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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [http://pdbe.org/1uke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [http://www.ebi.ac.uk/pdbsum/1uke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1uke ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 38:		Line 38:
	</StructureSection>		</StructureSection>
	[[Category: Atcc 11735]]		[[Category: Atcc 11735]]
			[[Category: Large Structures]]
	[[Category: UMP/CMP kinase]]		[[Category: UMP/CMP kinase]]
	[[Category: Kliche, W]]		[[Category: Kliche, W]]

OCA at 07:57, 28 March 2018

2018-03-28T07:57:30Z

← Older revision		Revision as of 07:57, 28 March 2018
Line 1:		Line 1:

	==UMP/CMP KINASE FROM SLIME MOLD==		==UMP/CMP KINASE FROM SLIME MOLD==
	<StructureSection load='1uke' size='340' side='right' caption='[[1uke]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1uke' size='340' side='right' caption='[[1uke]], [[Resolution\|resolution]] 2.20Å' scene=''>
Line 6:		Line 7:
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 ATCC 11735])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 ATCC 11735])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [http://pdbe.org/1uke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [http://www.ebi.ac.uk/pdbsum/1uke 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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [http://pdbe.org/1uke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [http://www.ebi.ac.uk/pdbsum/1uke PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1uke ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 14:		Line 15:
	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uk/1uke_consurf.spt"</scriptWhenChecked>		<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/uk/1uke_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 29:		Line 30:
	</div>		</div>
	<div class="pdbe-citations 1uke" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1uke" style="background-color:#fffaf0;"></div>

			==See Also==
			*[[UMP/CMP kinase\|UMP/CMP kinase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 11:12, 7 February 2016

2016-02-07T11:12:25Z

← Older revision		Revision as of 11:12, 7 February 2016
Line 18:		Line 18:
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</jmolCheckbox>
	</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].		</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary\|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1uke ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 00:56, 10 September 2015

2015-09-10T00:56:44Z

← Older revision		Revision as of 00:56, 10 September 2015
Line 2:		Line 2:
	<StructureSection load='1uke' size='340' side='right' caption='[[1uke]], [[Resolution\|resolution]] 2.20Å' scene=''>		<StructureSection load='1uke' size='340' side='right' caption='[[1uke]], [[Resolution\|resolution]] 2.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1uke]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/~~Dictyostelium_discoideum Dictyostelium discoideum~~]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UKE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1uke]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_11735 Atcc 11735]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UKE FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UP5:P1-(ADENOSINE-5-P5-(URIDINE-5)PENTAPHOSPHATE'>UP5</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UP5:P1-(ADENOSINE-5-P5-(URIDINE-5)PENTAPHOSPHATE'>UP5</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 ~~Dictyostelium discoideum~~])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 ATCC 11735])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/~~Cytidylate_kinase Cytidylate~~ kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/UMP/CMP_kinase UMP/CMP kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [http://www.ebi.ac.uk/pdbsum/1uke 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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [http://pdbe.org/1uke PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [http://www.ebi.ac.uk/pdbsum/1uke PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
Line 28:		Line 28:
	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
			<div class="pdbe-citations 1uke" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
	[[Category: ~~Cytidylate kinase~~]]		[[Category: Atcc 11735]]
	[[Category: ~~Dictyostelium discoideum~~]]		[[Category: UMP/CMP kinase]]
	[[Category: Kliche, W]]		[[Category: Kliche, W]]
	[[Category: Reinstein, J]]		[[Category: Reinstein, J]]

OCA at 14:38, 24 December 2014

2014-12-24T14:38:51Z

← Older revision		Revision as of 14:38, 24 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1uke]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UKE FirstGlance]. <br>		<table><tr><td colspan='2'>[[1uke]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UKE FirstGlance]. <br>
	</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UP5:P1-(ADENOSINE-5-P5-(URIDINE-5)PENTAPHOSPHATE'>UP5</scene><br>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UP5:P1-(ADENOSINE-5-P5-(URIDINE-5)PENTAPHOSPHATE'>UP5</scene></td></tr>
	<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 Dictyostelium discoideum])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 Dictyostelium discoideum])</td></tr>
	<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytidylate_kinase Cytidylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytidylate_kinase Cytidylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [http://www.ebi.ac.uk/pdbsum/1uke 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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [http://www.ebi.ac.uk/pdbsum/1uke PDBsum]</span></td></tr>
	<table>		</table>
			== Function ==
			[[http://www.uniprot.org/uniprot/KCY_DICDI KCY_DICDI]] This UMP-CMP kinase uses preferentially ATP as phosphate donor and is specific for UMP and CMP.
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 32:		Line 34:
	[[Category: Cytidylate kinase]]		[[Category: Cytidylate kinase]]
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
	[[Category: Kliche, W.]]		[[Category: Kliche, W]]
	[[Category: Reinstein, J.]]		[[Category: Reinstein, J]]
	[[Category: Scheffzek, K.]]		[[Category: Scheffzek, K]]
	[[Category: Wiesmueller, L.]]		[[Category: Wiesmueller, L]]
	[[Category: Bisubstrate inhibitor]]		[[Category: Bisubstrate inhibitor]]
	[[Category: Nmp kinase]]		[[Category: Nmp kinase]]

OCA at 20:33, 29 September 2014

2014-09-29T20:33:17Z

← Older revision		Revision as of 20:33, 29 September 2014
Line 1:		Line 1:
	[[Image:~~1uke~~.~~png~~\|~~left~~\|~~200px~~]]		==UMP/CMP KINASE FROM SLIME MOLD==
			<StructureSection load='1uke' size='340' side='right' caption='[[1uke]], [[Resolution\|resolution]] 2.20Å' scene=''>
			== Structural highlights ==
			<table><tr><td colspan='2'>[[1uke]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1UKE FirstGlance]. <br>
			</td></tr><tr><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UP5:P1-(ADENOSINE-5-P5-(URIDINE-5)PENTAPHOSPHATE'>UP5</scene><br>
			<tr><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 Dictyostelium discoideum])</td></tr>
			<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytidylate_kinase Cytidylate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.14 2.7.4.14] </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=1uke FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uke OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1uke RCSB], [http://www.ebi.ac.uk/pdbsum/1uke 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/uk/1uke_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 ==
			The three-dimensional structure of the UMP/CMP kinase (UK) from the slime mold Dictyostelium discoideum complexed with the specific and asymmetric bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) has been determined at a resolution of 2.2 A. The structure of the enzyme, which has up to 41% sequence homology with known adenylate kinases (AK), represents a closed conformation with the flexible monophosphate binding domain (NMP site) being closed over the uridyl moiety of the dinucleotide. Two water molecules were found within hydrogen-bonding distance to the uracil base. The key residue for the positioning and stabilization of those water molecules appears to be asparagine 97, a residue that is highly specific for AK-homologous UMP kinases, but is almost invariably a glutamine in adenylate kinases. Other residues in this region are highly conserved among AK-related NMP kinases. The catalytic Mg2+ ion is coordinated with octahedral geometry to four water molecules and two oxygens of the phosphate chain of UP5A but has no direct interactions with the protein. The comparison of the geometry of the UKdicty.UP5A.Mg2+ complex with the previously reported structure of the UKyeast.ADP.ADP complex [Muller-Dieckmann & Schulz (1994) J. Mol. Biol. 236, 361-367] suggests that UP5A in our structure mimics an ADP.Mg.UDP biproduct inhibitor rather than an ATP. MG.UMP bisubstrate inhibitor.

	~~{{STRUCTURE_1uke\| PDB=1uke \| SCENE= }}~~		Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity.,Scheffzek K, Kliche W, Wiesmuller L, Reinstein J Biochemistry. 1996 Jul 30;35(30):9716-27. PMID:8703943<ref>PMID:8703943</ref>

	~~===UMP~~/~~CMP KINASE FROM SLIME MOLD===~~		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
	~~{{ABSTRACT_PUBMED_8703943}}~~		== References ==
			<references/>
	~~==About this Structure==~~		__TOC__
	~~[[1uke]] is~~ a ~~1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. This structure supersedes~~ the ~~now removed PDB entry [http://oca~~.~~weizmann~~.ac.il/~~oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA].~~		</StructureSection>

	==~~Reference~~==
	<~~ref group="xtra">PMID:008703943<~~/~~ref~~><~~references group="xtra"~~/>
	[[Category: Cytidylate kinase]]		[[Category: Cytidylate kinase]]
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]

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

2013-01-05T11:17:24Z

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

← Older revision	Revision as of 11:17, 5 January 2013
(No difference)

OCA at 11:17, 5 January 2013

2013-01-05T11:17:21Z

← Older revision		Revision as of 11:17, 5 January 2013
Line 1:		Line 1:
	~~{{Seed}}~~
	[[Image:1uke.png\|left\|200px]]		[[Image:1uke.png\|left\|200px]]

	~~<!--~~
	~~The line below this paragraph, containing "STRUCTURE_1uke", 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_1uke\| PDB=1uke \| SCENE= }}		{{STRUCTURE_1uke\| PDB=1uke \| SCENE= }}

	===UMP/CMP KINASE FROM SLIME MOLD===		===UMP/CMP KINASE FROM SLIME MOLD===


	~~<!--~~
	~~The line below this paragraph, {{ABSTRACT_PUBMED_8703943}}, adds the Publication Abstract to the page~~
	~~(as it appears on PubMed at http://www.pubmed.gov), where 8703943 is the PubMed ID number.~~
	~~-->~~
	{{ABSTRACT_PUBMED_8703943}}		{{ABSTRACT_PUBMED_8703943}}

	==About this Structure==		==About this Structure==
	~~1UKE~~ is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA].		[[1uke]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA].

	==Reference==		==Reference==
	<ref group="xtra">PMID:~~8703943~~</ref><references group="xtra"/>		<ref group="xtra">PMID:008703943</ref><references group="xtra"/>
	[[Category: Cytidylate kinase]]		[[Category: Cytidylate kinase]]
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
Line 35:		Line 23:
	[[Category: Nucleotide specificity]]		[[Category: Nucleotide specificity]]
	[[Category: Phosphoryl transfer]]		[[Category: Phosphoryl transfer]]

	~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:25:08 2009''~~

OCA at 11:25, 16 February 2009

2009-02-16T11:25:09Z

← Older revision		Revision as of 11:25, 16 February 2009
Line 20:		Line 20:

	==About this Structure==		==About this Structure==
	1UKE is a ~~[[Single protein]]~~ structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA].		1UKE is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1ukd 1ukd]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKE OCA].

	==Reference==		==Reference==
	Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity., Scheffzek K, Kliche W, Wiesmuller L, Reinstein J, Biochemistry. 1996 Jul 30;35(30):9716-27. PMID:~~[http:~~//~~www.ncbi.nlm.nih.gov/pubmed/8703943 8703943]~~		<ref group="xtra">PMID:8703943</ref><references group="xtra"/>
	[[Category: Cytidylate kinase]]		[[Category: Cytidylate kinase]]
	[[Category: Dictyostelium discoideum]]		[[Category: Dictyostelium discoideum]]
	~~[[Category: Single protein]]~~
	[[Category: Kliche, W.]]		[[Category: Kliche, W.]]
	[[Category: Reinstein, J.]]		[[Category: Reinstein, J.]]
Line 37:		Line 36:
	[[Category: Phosphoryl transfer]]		[[Category: Phosphoryl transfer]]

	''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on ~~Sun Jul 27 15~~:50:~~01 2008~~''		''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 13:25:08 2009''