184.108.40.206 - Nucleoside-diphosphate kinase
- Nucleoside diphosphokinase.
- Nucleoside 5'-diphosphate phosphotransferase.
2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-deoxyribonucleoside 5'-triphosphate + ADP
There are no Cofactors for this Enzyme
Nucleoside diphosphate kinase (NDP kinase) is responsible for phosphorylating non-adenine nucleoside diphosphates. The phosphate donor is usually ATP, but the diphosphate nucleotide substrate is non-specific for either base or ribose / deoxyribose.
The mechanism of nucleotide binding is different from that of most other phoshokinases and nucleotide binding proteins which use a parallel beta-sheet, NDP using an anti-parallel beta-sheet. NDPK from Dictyostelium discoideum is used as a model because it is particularly easy to crystallise.
NDPK operates using a 'ping-pong' mechanism. The gamma-phosphate of ATP is transferred to the delta-N atom of the doubly protonated His 122 of NDPK, with the delta-N proton concomitantly transferred to the gamma-phosphate. A nucleoside diphosphate binds in the active site. The phosphate group is transferred from His 122-P to the 5' hydroxyl of the ribose. Both phosphoryl transfers are dissociative SN2-like reactions, similar to the uncatalysed reaction.
The 3' ribose / deoxyribose hydroxyl group is more catalytically important than Tyr 56 or Lys 16; in the first transfer to His 122, it hydrogen bonds to the gamma-phosphate group, forcing the substrate into a reactive conformation and stabilising the negative charge by hydrogen bonding. The enzymatic reaction can therefore be described as substrate-assisted.
|AA||Uniprot||Uniprot Resid||PDB||PDB Resid|
overall reactant used, proton transfer, overall product formed, enzyme-substrate complex formation, intermediate formation, bimolecular nucleophilic substitution, intermediate terminated, native state of enzyme regenerated, intermediate collapse, enzyme-substrate complex cleavage
There are no kinetic parameters information for this Enzyme
- Direct and indirect targets of carboxyatractyloside, including overlooked toxicity toward nucleoside diphosphate kinase (NDPK) and mitochondrial H+ leak.
- Identifying inhibitors of Trypanosoma cruzi nucleoside diphosphate kinase 1 as potential repurposed drugs for Chagas' disease.
- The Mitochondrial Nucleoside Diphosphate Kinase NME4 Mediates Metabolic Reprogramming and Plays a Key Role in Nonalcoholic Fatty Liver Disease Progression
- In-silico structural characterization and phylogenetic analysis of Nucleoside diphosphate kinase: A novel antiapoptotic protein of Porphyromonas gingivalis.
- Insilico structural characterization and phylogenetic analysis of Nucleoside diphosphate kinase: A novel anti-apoptotic protein of Porphyromonas gingivalis
- Genetic defects in peroxisome morphogenesis (Pex11β, dynamin-like protein 1, and nucleoside diphosphate kinase 3) affect docosahexaenoic acid-phospholipid metabolism.
- Molecular docking and simulation studies against nucleoside diphosphate kinase (NDK) of Pseudomonas aeruginosa with secondary metabolite identified by genome mining from paenibacillusehimensis.
- The Mechanism of Action of Lactoferrin - Nucleoside Diphosphate Kinase Complex in Combating Biofilm Formation.
- Crystal structure and characterization of nucleoside diphosphate kinase from Vibrio cholerae.
- The mitochondrially-localized nucleoside diphosphate kinase D (NME4) is a novel metastasis suppressor.
- Leishmania donovani secretory protein nucleoside diphosphate kinase b localizes in its nucleus and prevents ATP mediated cytolysis of macrophages.