1uky: Difference between revisions

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-[[Image:1uky.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1uky", creates the "Structure Box" on the page.
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-{{STRUCTURE_1uky|  PDB=1uky  |  SCENE=  }}
-'''SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FROM TWO STRUCTURES OF LIGATED URIDYLATE KINASE'''
+==SUBSTRATE SPECIFICITY AND ASSEMBLY OF CATALYTIC CENTER DERIVED FROM TWO STRUCTURES OF LIGATED URIDYLATE KINASE==
+<StructureSection load='1uky' size='340' side='right'caption='[[1uky]], [[Resolution|resolution]] 2.13&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1uky]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UKY FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.13&#8491;</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></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=1uky FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uky OCA], [https://pdbe.org/1uky PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uky RCSB], [https://www.ebi.ac.uk/pdbsum/1uky PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uky ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/KCY_YEAST KCY_YEAST] Catalyzes the phosphorylation of pyrimidine nucleoside monophosphates at the expense of ATP. Plays an important role in de novo pyrimidine nucleotide biosynthesis. Has preference for UMP and dUMP as phosphate acceptors, but can also use CMP, dCMP, AMP, GMP, dGMP and dTMP. ATP and dATP are the best phosphate donors, but can also use GTP, dGTP, dCTP, and dTTP to some degree.<ref>PMID:1333436</ref> <ref>PMID:2172245</ref> <ref>PMID:8391780</ref> <ref>PMID:2549068</ref>
+== 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/1uky_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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/main_output.php?pdb_ID=1uky ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Two crystal structures of ligated uridylate kinase from Saccharomyces cerevisiae were determined by X-ray analyses. The ligands were ADP and AMP. Cocrystallization with ATP yielded crystals with ADP at the ATP site and a mixture of AMP and ADP at the NMP site. Cocrystallization with ADP gave rise to a distinct crystal type with ADP at the ATP site, but only AMP at the NMP site. In both cases, the substrates are kept in place by favorable crystal contacts. The structures have been refined to R-factors of 17.8% and 19.6% at resolutions of 2.1 A and 1.9 A, respectively. A comparison with the related cytosolic adenylate kinase from pig disclosed large induced-fit movements on substrate binding and the disassembly of the catalytic center in the absence of substrates. The relatively high side-activity of uridylate kinase for AMP is explained by the finding that the binding pocket is sized for an AMP, but constructed to bind UMP together with a water molecule.
-==Overview==
+Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase.,Muller-Dieckmann HJ, Schulz GE J Mol Biol. 1995 Mar 3;246(4):522-30. PMID:7877173<ref>PMID:7877173</ref>
-Two crystal structures of ligated uridylate kinase from Saccharomyces cerevisiae were determined by X-ray analyses. The ligands were ADP and AMP. Cocrystallization with ATP yielded crystals with ADP at the ATP site and a mixture of AMP and ADP at the NMP site. Cocrystallization with ADP gave rise to a distinct crystal type with ADP at the ATP site, but only AMP at the NMP site. In both cases, the substrates are kept in place by favorable crystal contacts. The structures have been refined to R-factors of 17.8% and 19.6% at resolutions of 2.1 A and 1.9 A, respectively. A comparison with the related cytosolic adenylate kinase from pig disclosed large induced-fit movements on substrate binding and the disassembly of the catalytic center in the absence of substrates. The relatively high side-activity of uridylate kinase for AMP is explained by the finding that the binding pocket is sized for an AMP, but constructed to bind UMP together with a water molecule.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-UKY is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UKY OCA].
+</div>
+<div class="pdbe-citations 1uky" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase., Muller-Dieckmann HJ, Schulz GE, J Mol Biol. 1995 Mar 3;246(4):522-30. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7877173 7877173]
+*[[Uridylate kinase|Uridylate kinase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Mueller-Dieckmann H-J]]
-[[Category: Mueller-Dieckmann, H J.]]
+[[Category: Schulz GE]]
-[[Category: Schulz, G E.]]
-[[Category: Transferase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 11:22:17 2008''