4ukd

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[[Image:4ukd.gif|left|200px]]
 
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{{Structure
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==UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM FLUORIDE==
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|PDB= 4ukd |SIZE=350|CAPTION= <scene name='initialview01'>4ukd</scene>, resolution 2.0&Aring;
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<StructureSection load='4ukd' size='340' side='right'caption='[[4ukd]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ADP:ADENOSINE-5&#39;-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5&#39;-DIPHOSPHATE'>UDP</scene>
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<table><tr><td colspan='2'>[[4ukd]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UKD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UKD FirstGlance]. <br>
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|ACTIVITY= <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>
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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]] 2&#8491;</td></tr>
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|GENE= KCY_DICDI ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=44689 Dictyostelium discoideum])
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<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>, <scene name='pdbligand=BF2:BERYLLIUM+DIFLUORIDE'>BF2</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=UDP:URIDINE-5-DIPHOSPHATE'>UDP</scene></td></tr>
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|DOMAIN=
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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=4ukd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ukd OCA], [https://pdbe.org/4ukd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ukd RCSB], [https://www.ebi.ac.uk/pdbsum/4ukd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ukd ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4ukd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ukd OCA], [http://www.ebi.ac.uk/pdbsum/4ukd PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=4ukd RCSB]</span>
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== Function ==
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}}
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[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.
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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/uk/4ukd_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=4ukd ConSurf].
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<div style="clear:both"></div>
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'''UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM FLUORIDE'''
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==See Also==
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*[[UMP/CMP kinase|UMP/CMP kinase]]
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__TOC__
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==Overview==
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</StructureSection>
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UMP/CMP kinase from Dictyostelium discoideum (UmpKdicty) catalyzes the specific transfer of the terminal phosphate of ATP to UMP or CMP. Crystal structures of UmpKdicty with substrates and the transition state analogs AlF3 or BeF2 that lock UmpKdicty in active conformations were solved. The positions of the catalytic Mg2+ and the highly conserved lysine of the P loop are virtually invariant in the different structures. In contrast, catalytic arginines move to stabilize charges that develop during this reaction. The location of the arginines indicates formation of negative charges during the reaction at the transferred phosphoryl group, but not at the phosphate bridging oxygen atoms. This is consistent with an associative phosphoryl transfer mechanism but not with a dissociative one.
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==About this Structure==
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4UKD is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UKD OCA].
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==Reference==
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Structures of active conformations of UMP kinase from Dictyostelium discoideum suggest phosphoryl transfer is associative., Schlichting I, Reinstein J, Biochemistry. 1997 Aug 5;36(31):9290-6. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9280438 9280438]
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[[Category: Cytidylate kinase]]
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[[Category: Dictyostelium discoideum]]
[[Category: Dictyostelium discoideum]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Reinstein, J.]]
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[[Category: Reinstein J]]
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[[Category: Schlichting, I.]]
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[[Category: Schlichting I]]
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[[Category: nmp kinase]]
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[[Category: nucleoside monophosphate kinase]]
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[[Category: phosphoryl transfer]]
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[[Category: transferase]]
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[[Category: transition state analog complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 05:40:30 2008''
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Current revision

UMP/CMP KINASE FROM SLIME MOLD COMPLEXED WITH ADP, UDP, BERYLLIUM FLUORIDE

PDB ID 4ukd

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