3b54

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{{Seed}}
 
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[[Image:3b54.png|left|200px]]
 
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==Saccharomyces cerevisiae nucleoside diphosphate kinase==
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The line below this paragraph, containing "STRUCTURE_3b54", creates the "Structure Box" on the page.
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<StructureSection load='3b54' size='340' side='right'caption='[[3b54]], [[Resolution|resolution]] 3.10&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<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>
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or leave the SCENE parameter empty for the default display.
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</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>
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<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>
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{{STRUCTURE_3b54| PDB=3b54 | SCENE= }}
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<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>
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/b5/3b54_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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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=3b54 ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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===Saccharomyces cerevisiae nucleoside diphosphate kinase===
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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>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3b54" style="background-color:#fffaf0;"></div>
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==See Also==
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The line below this paragraph, {{ABSTRACT_PUBMED_18607079}}, adds the Publication Abstract to the page
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*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
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(as it appears on PubMed at http://www.pubmed.gov), where 18607079 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_18607079}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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3B54 is a 2 chains structure of sequences 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].
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==Reference==
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<ref group="xtra">PMID:18607079</ref><references group="xtra"/>
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[[Category: Nucleoside-diphosphate kinase]]
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[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Bao, R.]]
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[[Category: Bao R]]
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[[Category: Cheng, Y X.]]
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[[Category: Cheng YX]]
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[[Category: Wang, H B.]]
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[[Category: Wang HB]]
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[[Category: Alpha/beta sandwich]]
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[[Category: Atp-binding]]
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[[Category: Cytoplasm]]
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[[Category: Kinase]]
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[[Category: Magnesium]]
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[[Category: Metal-binding]]
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[[Category: Mitochondrion]]
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[[Category: Nucleotide metabolism]]
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[[Category: Nucleotide-binding]]
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[[Category: Phosphorylation]]
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[[Category: Transferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 16:22:13 2009''
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Current revision

Saccharomyces cerevisiae nucleoside diphosphate kinase

PDB ID 3b54

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