2zi9: Difference between revisions

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-[[Image:2zi9.png|left|200px]]
-{{STRUCTURE_2zi9|  PDB=2zi9  |  SCENE=  }}
+==C4S-E247A dCK variant of dCK in complex with cladribine+ADP==
+<StructureSection load='2zi9' size='340' side='right'caption='[[2zi9]], [[Resolution|resolution]] 2.51&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2zi9]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZI9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ZI9 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]] 2.51&#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>, <scene name='pdbligand=CL9:2-CHLORO-2-DEOXYADENOSINE'>CL9</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=2zi9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2zi9 OCA], [https://pdbe.org/2zi9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2zi9 RCSB], [https://www.ebi.ac.uk/pdbsum/2zi9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2zi9 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/DCK_HUMAN DCK_HUMAN] Required for the phosphorylation of the deoxyribonucleosides deoxycytidine (dC), deoxyguanosine (dG) and deoxyadenosine (dA). Has broad substrate specificity, and does not display selectivity based on the chirality of the substrate. It is also an essential enzyme for the phosphorylation of numerous nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:18377927</ref> <ref>PMID:20614893</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/zi/2zi9_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=2zi9 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Purine nucleoside analogues of medicinal importance, such as cladribine, require phosphorylation by deoxycytidine kinase (dCK) for pharmacological activity. Structural studies of ternary complexes of human dCK show that the enzyme conformation adjusts to the different hydrogen-bonding properties between dA and dG and to the presence of substituent at the 2-position present in dG and cladribine. Specifically, the carbonyl group in dG elicits a previously unseen conformational adjustment of the active site residues Arg104 and Asp133. In addition, dG and cladribine adopt the anti conformation, in contrast to the syn conformation observed with dA. Kinetic analysis reveals that cladribine is phosphorylated at the highest efficiency with UTP as donor. We attribute this to the ability of cladribine to combine advantageous properties from dA (favorable hydrogen-bonding pattern) and dG (propensity to bind to the enzyme in its anti conformation), suggesting that dA analogues with a substituent at the 2-position are likely to be better activated by human dCK.
-===C4S-E247A dCK variant of dCK in complex with cladribine+ADP===
+Elucidation of Different Binding Modes of Purine Nucleosides to Human Deoxycytidine Kinase.,Sabini E, Hazra S, Konrad M, Lavie A J Med Chem. 2008 Jun 21;. PMID:18570408<ref>PMID:18570408</ref>
-{{ABSTRACT_PUBMED_18570408}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2zi9" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2zi9]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ZI9 OCA].
+*[[Deoxycytidine kinase 3D structures|Deoxycytidine kinase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018570408</ref><references group="xtra"/>
+__TOC__
-[[Category: Deoxycytidine kinase]]
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Lavie, A.]]
+[[Category: Large Structures]]
-[[Category: Sabini, E.]]
+[[Category: Lavie A]]
-[[Category: Atp-binding]]
+[[Category: Sabini E]]
-[[Category: Cladribine]]
-[[Category: Dck]]
-[[Category: Deoxyadenosine analog]]
-[[Category: Deoxycytidine kinase]]
-[[Category: Nucleoside]]
-[[Category: Nucleotide-binding]]
-[[Category: Nucleus]]
-[[Category: Phosphoprotein]]
-[[Category: Purine]]
-[[Category: Transferase]]