4uoh

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==Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with ADP==
==Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with ADP==
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<StructureSection load='4uoh' size='340' side='right' caption='[[4uoh]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
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<StructureSection load='4uoh' size='340' side='right'caption='[[4uoh]], [[Resolution|resolution]] 2.01&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4uoh]] is a 3 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UOH OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4UOH FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4uoh]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Penaeus_vannamei Penaeus vannamei]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4UOH OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UOH FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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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]] 2.007&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4uof|4uof]], [[4uog|4uog]]</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=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></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=4uoh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoh OCA], [https://pdbe.org/4uoh PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uoh RCSB], [https://www.ebi.ac.uk/pdbsum/4uoh PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uoh ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4uoh FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uoh OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4uoh RCSB], [http://www.ebi.ac.uk/pdbsum/4uoh PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/A5J299_PENVA A5J299_PENVA]
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Nucleoside diphosphate kinase (NDK; EC 2.7.4.6) is an enzyme that catalyzes the third phosphorylation of nucleoside diphosphates, leading to nucleoside triphosphates for DNA replication. Expression of the NDK from Litopenaeus vannamei (LvNDK) is known to be regulated under viral infection. Also, as determined by isothermal titration calorimetry, LvNDK binds both purine and pyrimidine deoxynucleoside diphosphates with high binding affinity for dGDP and dADP and with no heat of binding interaction for dCDP [Quintero-Reyes et al. (2012), J. Bioenerg. Biomembr. 44, 325-331]. In order to investigate the differences in selectivity, LvNDK was crystallized as binary complexes with both acceptor (dADP and dCDP) and donor (ADP) phosphate-group nucleoside diphosphate substrates and their structures were determined. The three structures with purine or pyrimidine nucleotide ligands are all hexameric. Also, the binding of deoxy or ribonucleotides is similar, as in the former a water molecule replaces the hydrogen bond made by Lys11 to the 2'-hydroxyl group of the ribose moiety. This allows Lys11 to maintain a catalytically favourable conformation independently of the kind of sugar found in the nucleotide. Because of this, shrimp NDK may phosphorylate nucleotide analogues to inhibit the viral infections that attack this organism.
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Structure of nucleoside diphosphate kinase from pacific shrimp (Litopenaeus vannamei) in binary complexes with purine and pyrimidine nucleoside diphosphates.,Lopez-Zavala AA, Quintero-Reyes IE, Carrasco-Miranda JS, Stojanoff V, Weichsel A, Rudino-Pinera E, Sotelo-Mundo RR Acta Crystallogr F Struct Biol Commun. 2014 Sep 1;70(Pt 9):1150-4. doi:, 10.1107/S2053230X1401557X. Epub 2014 Aug 29. PMID:25195883<ref>PMID:25195883</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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==See Also==
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</div>
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*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Nucleoside-diphosphate kinase]]
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[[Category: Large Structures]]
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[[Category: Guevara-Hernandez, E]]
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[[Category: Penaeus vannamei]]
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[[Category: Lopez-Zavala, A A]]
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[[Category: Guevara-Hernandez E]]
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[[Category: Rudino-Pinera, E]]
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[[Category: Lopez-Zavala AA]]
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[[Category: Sotelo-Mundo, R R]]
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[[Category: Rudino-Pinera E]]
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[[Category: Stojanoff, V]]
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[[Category: Sotelo-Mundo RR]]
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[[Category: Adp]]
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[[Category: Stojanoff V]]
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[[Category: Binary]]
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[[Category: Binding site]]
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[[Category: Complex]]
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[[Category: Nucleotide]]
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[[Category: Purine]]
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[[Category: Transferase]]
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[[Category: White-shrimp]]
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Current revision

Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with ADP

PDB ID 4uoh

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