1uke: Difference between revisions

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 <StructureSection load='1uke' size='340' side='right'caption='[[1uke]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == 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]] 2.2&#8491;</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>
 == 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 ==
 [[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=1uke 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 &amp; 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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1uke" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[UMP/CMP kinase|UMP/CMP kinase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Atcc 11735]]
+[[Category: Dictyostelium discoideum]]
 [[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]]