4UOF

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

4UOF の概要

• エントリーDOI: 10.2210/pdb4uof/pdb
• 関連するPDBエントリー: 4UOG 4UOH
• 分子名称: NUCLEOSIDE DIPHOSPHATE KINASE, 2'-DEOXYADENOSINE-5'-DIPHOSPHATE, MAGNESIUM ION, ... (4 entities in total)
• 機能のキーワード: transferase, binary, complex, dadp, purine, white-shrimp, binding site, desoxynucleotide
• 由来する生物種: LITOPENAEUS VANNAMEI (PACIFIC WHITE SHRIMP)
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 52353.40

構造登録者

Lopez-Zavala, A.A.,Stojanoff, V.,Rudino-Pinera, E.,Sotelo-Mundo, R.R. (登録日: 2014-06-03, 公開日: 2014-09-10, 最終更新日: 2024-01-10)

主引用文献

Lopez-Zavala, A.A.,Quintero-Reyez, I.E.,Carrasco-Miranda, J.S.,Stojanoff, V.,Weichsel, A.,Rudino-Pinera, E.,Sotelo-Mundo, R.R.
Structure of Nucleoside Diphosphate Kinase from the Pacific Shrimp (Litopenaeus Vannamei) in Binary Complexes with Purine and Pyrimidine Nucleoside Diphosphates
Acta Crystallogr.,Sect.F, 79:1150-, 2014

PubMed Abstract: 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.

PubMed: 25195883
DOI: 10.1107/S2053230X1401557X

実験手法

X-RAY DIFFRACTION (2.102 Å)