3b54: Difference between revisions

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-[[Image:3b54.png|left|200px]]
-{{STRUCTURE_3b54|  PDB=3b54  |  SCENE=  }}
+==Saccharomyces cerevisiae nucleoside diphosphate kinase==
+<StructureSection load='3b54' size='340' side='right'caption='[[3b54]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3b54]] is a 2 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=3B54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B54 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]] 3.1&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=3b54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b54 OCA], [https://pdbe.org/3b54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b54 RCSB], [https://www.ebi.ac.uk/pdbsum/3b54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b54 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NDK_YEAST NDK_YEAST] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. Required for repair of UV radiation- and etoposide-induced DNA damage.<ref>PMID:18983998</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/b5/3b54_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/main_output.php?pdb_ID=3b54 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Nucleoside diphosphate kinase (NDPK) catalyzes the transfer of the gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. In addition to biochemical studies, a number of crystal structures of NDPK from various organisms, including both native proteins and complexes with nucleotides or nucleotide analogues, have been determined. Here, the crystal structure of Ynk1, an NDPK from the yeast Saccharomyces cerevisiae, has been solved at 3.1 A resolution. Structural analysis strongly supports the oligomerization state of this protein being hexameric rather than tetrameric.
-===Saccharomyces cerevisiae nucleoside diphosphate kinase===
+Structure of Ynk1 from the yeast Saccharomyces cerevisiae.,Wang H, Bao R, Jiang C, Yang Z, Zhou CZ, Chen Y Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jul 1;64(Pt, 7):572-6. Epub 2008 Jun 28. PMID:18607079<ref>PMID:18607079</ref>
-{{ABSTRACT_PUBMED_18607079}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3b54" style="background-color:#fffaf0;"></div>
-[[3b54]] is a 2 chain structure of [[Nucleoside diphosphate kinase]] with 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=3B54 OCA].
 ==See Also==
-*[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]]
+*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018607079</ref><references group="xtra"/>
+__TOC__
-[[Category: Nucleoside-diphosphate kinase]]
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Bao, R.]]
+[[Category: Bao R]]
-[[Category: Cheng, Y X.]]
+[[Category: Cheng YX]]
-[[Category: Wang, H B.]]
+[[Category: Wang HB]]
-[[Category: Alpha/beta sandwich]]
-[[Category: Atp-binding]]
-[[Category: Kinase]]
-[[Category: Magnesium]]
-[[Category: Metal-binding]]
-[[Category: Mitochondrion]]
-[[Category: Nucleotide metabolism]]
-[[Category: Nucleotide-binding]]
-[[Category: Phosphorylation]]
-[[Category: Transferase]]