Cloned (Comment) | Organism |
---|---|
functional recombinant expression in Escherichia coli | Penaeus vannamei |
Crystallization (Comment) | Organism |
---|---|
purified recombinant enzyme in binary complexes with purine and pyrimidine nucleoside diphosphates, acceptors dADP and dCDP and donor ADP, mixing of 0.001 ml of 20 mg/ml protein in 100 mM NaCl, 40 mM MgCl2, 4mM DTT, and 20 mM nucleotides with 0.001 ml of reservoir solution containing 0.2 M magnesium chloride hexahydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG 4000 or 0.2 M sodium acetate trihydrate, 0.1 M Tris-HCl, pH 8.5, 30% w/v PEG 4000, or 0.2 M ammonium acetate, 0.1 M Tris-HCl, pH 8.5, 30% v/v 2-propanol, 3-7 days, 16°C, X-ray diffraction structure determination and analysis at 2.0-2.3 A resolution, molecular replacement | Penaeus vannamei |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Mg2+ | required | Penaeus vannamei |
Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
---|---|---|---|
57000 | - |
about, trimeric enzyme in solution | Penaeus vannamei |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
ATP + nucleoside diphosphate | Penaeus vannamei | this reaction is a reversible phosphate transfer to both ribonucleoside and deoxyribonucleoside diphosphates using NTP as a phosphate donor to provide adequate nucleosides for RNA or DNA synthesis | ADP + nucleoside triphosphate | - |
r |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Penaeus vannamei | A5J299 | - |
- |
Purification (Comment) | Organism |
---|---|
recombinant enzyme from Escherichia coli | Penaeus vannamei |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate | the reaction catalyzed by NDK starts with the transfer of a phosphate from ATP to His117. ADP is then released and the acceptor nucleoside diphosphate is bound and phosphorylated. Nucleotide phosphates are coordinated by a network of basic Arg and His residues, and a polar Thr. All NDKs follow a ping-pong enzymatic mechanism involving a phosphorylated histidine residue in the active site | Penaeus vannamei |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
ADP + dADP | - |
Penaeus vannamei | AMP + dATP | - |
r | |
ADP + dCDP | low activity | Penaeus vannamei | AMP + dCTP | - |
r | |
ADP + dGDP | - |
Penaeus vannamei | AMP + dGTP | - |
r | |
ATP + nucleoside diphosphate | - |
Penaeus vannamei | ADP + nucleoside triphosphate | - |
r | |
ATP + nucleoside diphosphate | this reaction is a reversible phosphate transfer to both ribonucleoside and deoxyribonucleoside diphosphates using NTP as a phosphate donor to provide adequate nucleosides for RNA or DNA synthesis | Penaeus vannamei | ADP + nucleoside triphosphate | - |
r | |
additional information | enzyme LvNDK has relaxed substrate specificity and binds both purine and pyrimidine deoxynucleoside diphosphates with high binding affinity for dGDP and dADP and with low binding interaction for dCDP. The binding of deoxy- or ribonucleotides is similar, as in the former a water molecule replaces the hydrogen bond made by Lys11 to the 20-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 | Penaeus vannamei | ? | - |
? |
Subunits | Comment | Organism |
---|---|---|
hexamer | crystal structure analysis | Penaeus vannamei |
trimer | in solution | Penaeus vannamei |
Synonyms | Comment | Organism |
---|---|---|
NDK | - |
Penaeus vannamei |
nucleoside diphosphate kinase | - |
Penaeus vannamei |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
ATP | - |
Penaeus vannamei |
Organism | Comment | Expression |
---|---|---|
Penaeus vannamei | the NDK enzyme expression is regulated under viral infection | additional information |
General Information | Comment | Organism |
---|---|---|
additional information | LvNDK has a nucleotide-binding site and a catalytic histidine nucleophile His117, which is part of a phosphorelay that transfers a phosphoryl group obtained from ATP to the nucleoside diphosphate, substrate binding structures, overview | Penaeus vannamei |
physiological function | the enzyme catalyzes the third phosphorylation of nucleoside diphosphates, leading to nucleoside triphosphates for DNA replication. Enzyme NDK may phosphorylate nucleotide analogues to inhibit the viral infections that attack this organism | Penaeus vannamei |