2a30: Difference between revisions

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-[[Image:2a30.png|left|200px]]
-{{STRUCTURE_2a30|  PDB=2a30  |  SCENE=  }}
+==Crystal structure of human deoxycytidine kinase in complex with deoxycytidine==
+<StructureSection load='2a30' size='340' side='right'caption='[[2a30]], [[Resolution|resolution]] 3.02&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2a30]] is a 4 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=2A30 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A30 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]] 3.02&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=DCZ:2-DEOXYCYTIDINE'>DCZ</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=2a30 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a30 OCA], [https://pdbe.org/2a30 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a30 RCSB], [https://www.ebi.ac.uk/pdbsum/2a30 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a30 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/a3/2a30_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=2a30 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Human deoxycytidine kinase (dCK) uses nucleoside triphosphates to phosphorylate several clinically important prodrugs in addition to its natural substrates. Although UTP is the preferred phosphoryl donor for this reaction, our previous studies reported dCK structures solely containing ADP in the phosphoryl donor binding site. To determine the molecular basis of the kinetically observed phosphoryl donor preference, we solved crystal structures of a dCK variant lacking a flexible insert (residues 65-79) but having similar catalytic properties as wild type, in complex with deoxycytidine (dC) and UDP, and in the presence of dC but the absence of UDP or ADP. These structures reveal major changes in the donor base binding loop (residues 240-247) between the UDP-bound and ADP-bound forms, involving significant main-chain rearrangement. This loop is disordered in the dCK-dC structure, which lacks a ligand at the phosphoryl donor site. In comparison with the ADP-bound form, in the presence of UDP this loop is shifted inward to make closer contact to the smaller uracil base. These structures illuminate the phosphoryl donor binding and preference mechanisms of dCK.
-===Crystal structure of human deoxycytidine kinase in complex with deoxycytidine===
+Structural basis for the preference of UTP over ATP in human deoxycytidine kinase: illuminating the role of main-chain reorganization.,Godsey MH, Ort S, Sabini E, Konrad M, Lavie A Biochemistry. 2006 Jan 17;45(2):452-61. PMID:16401075<ref>PMID:16401075</ref>
-{{ABSTRACT_PUBMED_16401075}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2a30" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-[[2a30]] is a 4 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=2A30 OCA].
+*[[Deoxycytidine kinase 3D structures|Deoxycytidine kinase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:016401075</ref><references group="xtra"/>
+__TOC__
-[[Category: Deoxycytidine kinase]]
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Godsey, M H.]]
+[[Category: Large Structures]]
-[[Category: Konrad, M.]]
+[[Category: Godsey MH]]
-[[Category: Lavie, A.]]
+[[Category: Konrad M]]
-[[Category: Ort, S.]]
+[[Category: Lavie A]]
-[[Category: Sabini, E.]]
+[[Category: Ort S]]
-[[Category: Nucleoside kinase]]
+[[Category: Sabini E]]
-[[Category: Transferase]]