2ocp

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(New page: 200px<br /> <applet load="2ocp" size="450" color="white" frame="true" align="right" spinBox="true" caption="2ocp, resolution 2.80&Aring;" /> '''Crystal Structure o...)
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[[Image:2ocp.gif|left|200px]]<br />
 
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<applet load="2ocp" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2ocp, resolution 2.80&Aring;" />
 
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'''Crystal Structure of Human Deoxyguanosine Kinase'''<br />
 
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==Overview==
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==Crystal Structure of Human Deoxyguanosine Kinase==
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Deoxyribonucleoside kinases phosphorylate deoxyribonucleosides and, activate a number of medically important nucleoside analogs. Here we, report the structure of the Drosophila deoxyribonucleoside kinase with, deoxycytidine bound at the nucleoside binding site and that of the human, deoxyguanosine kinase with ATP at the nucleoside substrate binding site., Compared to the human kinase, the Drosophila kinase has a wider substrate, cleft, which may be responsible for the broad substrate specificity of, this enzyme. The human deoxyguanosine kinase is highly specific for purine, substrates; this is apparently due to the presence of Arg 118, which, provides favorable hydrogen bonding interactions with the substrate. The, two new structures provide an explanation for the substrate specificity of, cellular deoxyribonucleoside kinases.
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<StructureSection load='2ocp' size='340' side='right'caption='[[2ocp]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2ocp]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1jag 1jag]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OCP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2OCP FirstGlance]. <br>
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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]] 2.8&#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=DTP:2-DEOXYADENOSINE+5-TRIPHOSPHATE'>DTP</scene></td></tr>
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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=2ocp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ocp OCA], [https://pdbe.org/2ocp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ocp RCSB], [https://www.ebi.ac.uk/pdbsum/2ocp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ocp ProSAT]</span></td></tr>
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</table>
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== Disease ==
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[https://www.uniprot.org/uniprot/DGUOK_HUMAN DGUOK_HUMAN] Defects in DGUOK are the cause of mitochondrial DNA depletion syndrome type 3 (MTDPS3) [MIM:[https://omim.org/entry/251880 251880]. A disorder characterized by onset in infancy of progressive liver failure, hypoglycemia, increased lactate in body fluids, and neurologic abnormalities including hypotonia, encephalopathy, peripheral neuropathy. Affected tissues show both decreased activity of the mtDNA-encoded respiratory chain complexes and mtDNA depletion.<ref>PMID:12205643</ref> <ref>PMID:15639197</ref>
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== Function ==
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[https://www.uniprot.org/uniprot/DGUOK_HUMAN DGUOK_HUMAN] Required for the phosphorylation of several deoxyribonucleosides and certain nucleoside analogs widely employed as antiviral and chemotherapeutic agents.<ref>PMID:8706825</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/oc/2ocp_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=2ocp 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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Deoxyribonucleoside kinases phosphorylate deoxyribonucleosides and activate a number of medically important nucleoside analogs. Here we report the structure of the Drosophila deoxyribonucleoside kinase with deoxycytidine bound at the nucleoside binding site and that of the human deoxyguanosine kinase with ATP at the nucleoside substrate binding site. Compared to the human kinase, the Drosophila kinase has a wider substrate cleft, which may be responsible for the broad substrate specificity of this enzyme. The human deoxyguanosine kinase is highly specific for purine substrates; this is apparently due to the presence of Arg 118, which provides favorable hydrogen bonding interactions with the substrate. The two new structures provide an explanation for the substrate specificity of cellular deoxyribonucleoside kinases.
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==Disease==
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Structural basis for substrate specificities of cellular deoxyribonucleoside kinases.,Johansson K, Ramaswamy S, Ljungcrantz C, Knecht W, Piskur J, Munch-Petersen B, Eriksson S, Eklund H Nat Struct Biol. 2001 Jul;8(7):616-20. PMID:11427893<ref>PMID:11427893</ref>
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Known diseases associated with this structure: Mitochondrial DNA-depletion syndrome, hepatocerebral form OMIM:[[http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id=601465 601465]]
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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2OCP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with DTP as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1JAG. Active as [http://en.wikipedia.org/wiki/Deoxyguanosine_kinase Deoxyguanosine kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.1.113 2.7.1.113] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2OCP OCA].
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</div>
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<div class="pdbe-citations 2ocp" style="background-color:#fffaf0;"></div>
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==Reference==
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== References ==
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Structural basis for substrate specificities of cellular deoxyribonucleoside kinases., Johansson K, Ramaswamy S, Ljungcrantz C, Knecht W, Piskur J, Munch-Petersen B, Eriksson S, Eklund H, Nat Struct Biol. 2001 Jul;8(7):616-20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11427893 11427893]
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<references/>
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[[Category: Deoxyguanosine kinase]]
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__TOC__
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</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Eklund, H.]]
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[[Category: Eklund H]]
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[[Category: Eriksson, S.]]
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[[Category: Eriksson S]]
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[[Category: Johansson, K.]]
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[[Category: Johansson K]]
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[[Category: Knecht, W.]]
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[[Category: Knecht W]]
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[[Category: Ljungkrantz, C.]]
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[[Category: Ljungkrantz C]]
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[[Category: Munch-Petersen, B.]]
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[[Category: Munch-Petersen B]]
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[[Category: Piskur, J.]]
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[[Category: Piskur J]]
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[[Category: Ramaswamy, S.]]
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[[Category: Ramaswamy S]]
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[[Category: DTP]]
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[[Category: protein-nucleotide complex]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 23:09:16 2007''
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Current revision

Crystal Structure of Human Deoxyguanosine Kinase

PDB ID 2ocp

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