4uog: Difference between revisions
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The | ==Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with dCDP== | ||
<StructureSection load='4uog' size='340' side='right'caption='[[4uog]], [[Resolution|resolution]] 2.30Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4uog]] 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=4UOG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4UOG 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]] 2.3Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=YYY:DEOXYCYTIDINE+DIPHOSPHATE'>YYY</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=4uog FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4uog OCA], [https://pdbe.org/4uog PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4uog RCSB], [https://www.ebi.ac.uk/pdbsum/4uog PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4uog ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/A5J299_PENVA A5J299_PENVA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 4uog" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Penaeus vannamei]] | |||
[[Category: Lopez-Zavala AA]] | |||
[[Category: Rudino-Pinera E]] | |||
[[Category: Sotelo-Mundo RR]] | |||
[[Category: Stojanoff V]] | |||
Latest revision as of 13:31, 10 January 2024
Crystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with dCDPCrystallographic structure of nucleoside diphosphate kinase from Litopenaeus vannamei complexed with dCDP
Structural highlights
FunctionPublication Abstract from PubMedNucleoside 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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