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Information on EC 2.7.4.6 - nucleoside-diphosphate kinase and Organism(s) Dictyostelium discoideum and UniProt Accession P22887

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IUBMB Comments
Many nucleoside diphosphates can act as acceptors, while many ribo- and deoxyribonucleoside triphosphates can act as donors.
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This record set is specific for:
Dictyostelium discoideum
UNIPROT: P22887
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The taxonomic range for the selected organisms is: Dictyostelium discoideum
The enzyme appears in selected viruses and cellular organisms
Synonyms
nm23-h1, nucleoside diphosphate kinase, ndp kinase, nm23-h2, ndpk-b, ndpk2, nucleoside diphosphokinase, ndk-1, nucleoside-diphosphate kinase, nucleoside diphosphate kinase a, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
kinase, nucleoside diphosphate (phosphorylating)
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NDK
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nucleoside 5'-diphosphate kinase
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nucleoside diphosphate (UDP) kinase
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nucleoside diphosphate kinase C
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nucleoside diphosphokinase
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nucleotide phosphate kinase
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UDP kinase
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uridine diphosphate kinase
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REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
show the reaction diagram
mechanism
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
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SYSTEMATIC NAME
IUBMB Comments
ATP:nucleoside-diphosphate phosphotransferase
Many nucleoside diphosphates can act as acceptors, while many ribo- and deoxyribonucleoside triphosphates can act as donors.
CAS REGISTRY NUMBER
COMMENTARY hide
9026-51-1
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2',3'-dehydro-3'-deoxyTDP + ATP
2',3'-dehydro-3'-deoxyTTP + ADP
show the reaction diagram
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?
3'-fluoro-2',3'-dideoxyUDP + ATP
3'-fluoro-2',3'-dideoxyUTP + ADP
show the reaction diagram
better than 2’,3’-dideoxyUDP, but much poorer than 2’-deoxyUDP
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?
3'-fluoro-3'-deoxyTDP + ATP
3'-fluoro-3'-deoxyTTP + ADP
show the reaction diagram
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?
ATP + dTDP
ADP + dTTP
show the reaction diagram
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?
NTP + nucleoside diphosphate
NDP + NTP
show the reaction diagram
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?
additional information
?
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strong preference for D-enantiomers of antiviral nucleotide analogs like ddATP, ddCTP, 3'-deoxy-3'-thymidine, 2',3'-didehydro-2',3'-dideoxythymidine
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?
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
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the enzyme colocalises with actin and calmodulin, but not with macropinosomes
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
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the enzyme inhibits phagocytosis (but not amoeboid motility) and macropinocytosis which contrasts with its positive regulatory role in micropinocytosis. The enzyme has no effect on multicellular development and promotes growth in liquid
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
NDKC_DICDI
155
0
16794
Swiss-Prot
other Location (Reliability: 2)
PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
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crystal structure
additional information
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overview on enzyme structure
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with 3’-fluoro-2’,3’-dideoxyUDP
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H122G
study of chemical rescue for ATP attack, crystallization data
K16A
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specific activity drastically reduced
K16R
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specific activity drastically reduced
Y56A
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specific activity drastically reduced
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
room temperature, several h
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in E. coli
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
cloned and expressed in Escherichia coli
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
low affinity of enzyme for L-dideoxynucleoside triphosphates, implications for antiviral therapies and treatment of AIDS
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Dumas, C.; Lebras, G.; Wallet, V.; Lacombe, M.L.; Vron, M.; Janin, J.
Crystallization and preliminary X-ray diffraction studies of nucleoside diphosphate kinase from Dictyostelium discoideum
J. Mol. Biol.
217
239-240
1991
Dictyostelium discoideum
Manually annotated by BRENDA team
Schneider, B.; Babolat, M.; Xu, Y.W.; Janin, J.; Veron, M.; Deville-Bonne, D.
Mechanism of phosphoryl transfer by nucleoside diphosphate kinase pH dependence and role of the active site Lys16 and Tyr56 residues
Eur. J. Biochem.
268
1964-1971
2001
Dictyostelium discoideum
Manually annotated by BRENDA team
Gonin, P.; Xu, Y.; Milon, L.; Dabernat, S.; Morr, M.; Kumar, R.; Lacombe, M.L.; Janin, J.; Lascu, I.
Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography
Biochemistry
38
7265-7272
1999
Dictyostelium discoideum (P22887)
Manually annotated by BRENDA team
Admiraal, S.J.; Schneider, B.; Meyer, P.; Janin, J.; Veron, M.; Deville-Bonne, D.; Herschlag, D.
Nucleophilic Activation by Positioning in Phosphoryl Transfer Catalyzed by Nucleoside Diphosphate Kinase
Biochemistry
38
4701-4711
1999
Dictyostelium discoideum (P22887)
Manually annotated by BRENDA team
Kreimeyer, A.; Schneider, B.; Sarfati, R.; Faraj, A.; Sommadossi, J.P.; Veron, M.; Deville-Bonne, D.
NDP kinase reactivity towards 3TC nucleotides
Antiviral Res.
50
147-156
2001
Dictyostelium discoideum (P22887)
Manually annotated by BRENDA team
Janin, J.; Deville-Bonne, D.
Nucleoside-diphosphate kinase: structural and kinetic analysis of reaction pathway and phosphohistidine intermediate
Methods Enzymol.
354
118-134
2002
Bos taurus, Dictyostelium discoideum, Drosophila melanogaster, Homo sapiens, Myxococcus xanthus, Rattus norvegicus
Manually annotated by BRENDA team
Annesley, S.J.; Bago, R.; Bosnar, M.H.; Filic, V.; Marinovi?, M.; Weber, I.; Mehta, A.; Fisher, P.R.
Dictyostelium discoideum nucleoside diphosphate kinase C plays a negative regulatory role in phagocytosis, macropinocytosis and exocytosis
PLoS ONE
6
e26024
2011
Dictyostelium discoideum, Dictyostelium discoideum AX2
Manually annotated by BRENDA team