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Information on EC 2.7.4.6 - nucleoside-diphosphate kinase and Organism(s) Pisum sativum and UniProt Accession Q9SP13
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2.7.4.6 nucleoside-diphosphate kinaseIUBMB Comments
Many nucleoside diphosphates can act as acceptors, while many ribo- and deoxyribonucleoside triphosphates can act as donors.
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Word Map
- 2.7.4.6
- triphosphate
- node
- gdp
- lymph
- adenylate
- metastases
- tumour
- autophosphorylation
- colorectal
- oncogene
- drosophila
- guanine
- c-myc
-
clinicopathological
- melanoma
- creatine
- dictyostelium
-
hexameric
-
gtp-binding
- discoideum
-
non-metastatic
-
gamma-phosphate
-
anti-metastatic
-
heterotrimeric
-
phosphohistidine
-
transphosphorylation
- dntp
- deoxyribonucleoside
- succinyl-coa
- phosphoenzyme
-
metastasis-related
- mastoparan
-
high-metastatic
-
metastasis-associated
-
prune
-
c-erbb-2
- myxococcus
-
g-quadruplexes
- deoxynucleoside
- xanthus
- medicine
- drug development
The taxonomic range for the selected organisms is: Pisum sativum
The enzyme appears in selected viruses and cellular organisms
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
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
kinase, nucleoside diphosphate (phosphorylating)
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-
-
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NDK
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-
-
-
NDPK
NDPK2
nucleoside 5'-diphosphate kinase
-
-
-
-
nucleoside diphosphate (UDP) kinase
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-
-
-
nucleoside diphosphate kinase
nucleoside diphosphokinase
-
-
-
-
nucleotide phosphate kinase
-
-
-
-
UDP kinase
-
-
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uridine diphosphate kinase
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-
-
-
additional information
additional information
the enzyme belongs to the nucleoside diphosphate kinase family
additional information
the enzyme belongs to the nucleoside diphosphate kinase family
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + nucleoside diphosphate = ADP + nucleoside triphosphate
phosphoenzyme intermediate with 2-4 mol phosphate per mol of enzyme
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phospho group transfer
-
-
-
-
PATHWAY SOURCE
PATHWAYS
KEGG
-
-, -, -, -, -, -, -, -, -, -, -, -, -, -, -, -, -
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
9026-51-1
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + dGDP
ADP + dGTP
dGDP is preferred over dTDP as an acceptor
-
-
?
ATP + NDP
ADP + NTP
contributes to the maintenance of the cellular pools of all nucleosides triphosphates, broad substrate specificity, in plants involved in different signaling pathways
-
-
?
NTP + nucleoside diphosphate
NDP + NTP
-
many ribo- and deoxyribonucleoside triphosphates act as donors
-
r
NTP + nucleoside diphosphate
NDP + NTP
-
trinucleotide substrates: ATP, CTP, GTP, ITP, dTTP, UTP, dCTP, dGTP
-
r
NTP + nucleoside diphosphate
NDP + NTP
-
substrates: 6-aza-UDP, 8-aza-GDP
-
r
NTP + nucleoside diphosphate
NDP + NTP
-
the broad specificity may reflect the presence of mixtures of isozymes of different reactivities with nucleotide substrates
-
r
NTP + nucleoside diphosphate
NDP + NTP
-
transfers gamma-phosphate from NTP to any nucleoside diphosphate
-
r
NTP + nucleoside diphosphate
NDP + NTP
-
dinucleotide substrates: ADP, CDP, GDP, UDP, IDP, dCDP, dGDP, dTDP
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r
additional information
?
-
-
enzyme additionally has nuclease activity cleaving supercoiled plasmid DNA, tRNAs or the 3UTR of atp9 mRNA. Nuclease- and kinase mechanisms are separate
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-
?
additional information
?
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key enzyme involved in the homeostasis of nucleoside triphosphates
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-
?
additional information
?
-
key enzyme involved in the homeostasis of nucleoside triphosphates
-
-
?
additional information
?
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-
nucleoside diphosphate kinase is responsible for maintaining the nucleotide balance in the cell, but is also involved in regulatory functions that often are mediated via protein-protein interactions, differentially for adenylate kinase isozymes, overview
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-
?
additional information
?
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-
NDPK3 protein additionally cleaves not only supercoiled plasmid DNA, but also highly structured RNA molecules such as tRNAs or the 3'UTR of the atp9 mRNA suggesting that the NDPK3 nuclease activity has a structural requirement, ATP inhibits this nuclease activity, while ADP has no effect, the nuclease- and the kinase-mechanisms are separate, overview
-
-
?
additional information
?
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-
protein-protein interaction analysis of adenylate kinases from Arabidopsis thaliana with the immobilized recombinant His-tagged NDPK from Pisum sativum, the interaction influences both enzyme activities, overview
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-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + NDP
ADP + NTP
contributes to the maintenance of the cellular pools of all nucleosides triphosphates, broad substrate specificity, in plants involved in different signaling pathways
-
-
?
additional information
?
-
-
key enzyme involved in the homeostasis of nucleoside triphosphates
-
-
?
additional information
?
-
key enzyme involved in the homeostasis of nucleoside triphosphates
-
-
?
additional information
?
-
-
nucleoside diphosphate kinase is responsible for maintaining the nucleotide balance in the cell, but is also involved in regulatory functions that often are mediated via protein-protein interactions, differentially for adenylate kinase isozymes, overview
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
divalent cation required for catalysis, Mg2+ preferred over other ions
Mn2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
adenylate kinase from Arabidopsis thaliana stimulates NDPK activity, whereas NDPK inhibits the activity of adenylate kinase, overview
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
103.5
line R3-1 isoform NDPK3, using dTDP as substrate, at pH 7.5 and 22°C
112.6
wild type isoform NDPK3, using dTDP as substrate, at pH 7.5 and 22°C
156.6
wild type isoform NDPK2, using dGDP as substrate, at pH 7.5 and 22°C
283.9
line R3-1 isoform NDPK2, using dGDP as substrate, at pH 7.5 and 22°C
41.3
wild type isoform NDPK2, using dTDP as substrate, at pH 7.5 and 22°C
63.98
line R3-1 isoform NDPK3, using dGDP as substrate, at pH 7.5 and 22°C
64.43
wild type isoform NDPK3, using dGDP as substrate, at pH 7.5 and 22°C
90.55
line R3-1 isoform NDPK2, using dTDP as substrate, at pH 7.5 and 22°C
additional information
-
specific activities of a variety of animals, plants and microorganisms
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
NDPK2 contains a predicted chloroplast targeting transit peptide of 63 amino acids, import mechanism, overview
additional information
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
there is a strong interaction between isoform NDPK2 and CAT1 in R3-1 plants, which possibly plays a vital role in the antioxidant defense against reactive oxygen species
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). Q9SP13_PEA
233
0
25264
TrEMBL
Mitochondrion (Reliability: 4)
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
16500
x * 16500, isoform NDPK3, calculated from amino acid sequence
17400
x * 25000, precursor protein, x * 18500, and x * 17400, mature enzyme forms
17600
x * 17600, low-molecular weight isoform NDPK2, calculated from amino acid sequence
18500
25000
additional information
18500
x * 25000, precursor protein, x * 18500, and x * 17400, mature enzyme forms
18500
x * 18500, mature form, SDS-PAGE, x * 25000, precursor form, SDS-PAGE
18500
x * 18500, high-molecular weight isoform NDPK2, calculated from amino acid sequence
25000
x * 25000, precursor protein, x * 18500, and x * 17400, mature enzyme forms
25000
x * 18500, mature form, SDS-PAGE, x * 25000, precursor form, SDS-PAGE
additional information
-
N-terminal sequence homology of kinases from different organisms
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hexamer
monomers are arranged as trimers of dimers, crystal structure analysis
?
x * 25000, precursor protein, x * 18500, and x * 17400, mature enzyme forms
?
x * 16500, isoform NDPK3, calculated from amino acid sequence
?
x * 17600, low-molecular weight isoform NDPK2, calculated from amino acid sequence
?
x * 18500, high-molecular weight isoform NDPK2, calculated from amino acid sequence
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
proteolytic modification
25000 Da, precursor protein, 18500 Da and 17400 Da, mature enzyme forms starting at amino acids 65 and 78 resp.
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
S69A
6% and 14% of wild type activity using dCDP or dTDP as substrate respectively, changes in subunit composition with increasing number of tetramers and dimers
A117D
-
complete loss of nucleoside diphosphate kinase activity, but no loss of nuclease activity
A77T
site-directed mutagenesis, the mutant shows an altered import behaviour into chloroplasts compared to the wild-type enzyme, overview
E205K
the mutation of isoform NDPK2 is associated with paraquat resistance
I12L
the mutation of isoform NDPK2 is associated with paraquat resistance
P45S
the mutation of isoform NDPK3 is associated with paraquat resistance
R63D
site-directed mutagenesis, the mutant shows an altered import behaviour into chloroplasts compared to the wild-type enzyme, overview
R74D
site-directed mutagenesis, the mutant shows an altered import behaviour into chloroplasts compared to the wild-type enzyme, overview
S69A
-
complete loss of nucleoside diphosphate kinase activity, but no loss of nuclease activity
additional information
-
immobiliztaion of the purified recombinant enzyme on N-hydroxysuccinimide HS-activated HP resin
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
glutathione Sepharose column chromatography, and gel filtration
native enzyme from chloroplasts to homogeneity, from cytosol and membranes
recombinant His-tagged NDPK from Escherichia coli by nickel affinity chromatography
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
transient expression of GFP-tagged wild-type and mutant NDPK2s in Pisum sativum protoplasts
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
isoform NDPK2 shows an increased level of activity and autophosphorylation in R3-1 plants compared to wild type plants
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Finan, P.M.; White, I.R.; Findlay, J.B.C.; Millner, P.A.
Identification of nucleoside diphosphate kinase from pea microsomal membrane
Biochem. Soc. Trans.
20
10S
1991
Pisum sativum
Parks, R.E.; Agarwal, R.P.
Nucleoside diphosphokinases
The Enzymes,3rd Ed. (Boyer,P. D. ,ed. )
8
307-333
1973
Anguilla rostrata, Avian myeloblastosis virus, Papio sp., Bacillus subtilis, Beta vulgaris subsp. vulgaris, Bos taurus, Saccharomyces cerevisiae, Vicia faba, Canis lupus familiaris, Gallus gallus, Columba livia, Oryctolagus cuniculus, Streptococcus pneumoniae, Escherichia coli, Felis catus, Helianthus tuberosus, Homo sapiens, Hordeum vulgare, Impatiens holstii, Micrococcus luteus, Platyrrhini, Mus musculus, Myxine glutinosa, Phoca vitulina, Pisum sativum, Rattus norvegicus, Saccharomyces pastorianus, Saccharum officinarum, Schistosoma mansoni, Solanum tuberosum, Squalus acanthias, Sus scrofa, Triticum aestivum
-
Johansson, M.; Mackenzie-Hose, A.; Andersson, I.; Knorpp, C.
Structure and mutational analysis of a plant mitochondrial nucleoside diphosphate kinase. Identification of residues involved in serine phosphorylation and oligomerization
Plant Physiol.
136
3034-3042
2004
Pisum sativum (Q9SP13)
Hammargren, J.; Salinas, T.; Marechal-Drouard, L.; Knorpp, C.
The pea mitochondrial nucleoside diphosphate kinase cleaves DNA and RNA
FEBS Lett.
581
3507-3511
2007
Pisum sativum
Sharma, R.; Soll, J.; Boelter, B.
Import and localisation of nucleoside diphosphate kinase 2 in chloroplasts
J. Plant Res.
120
451-456
2007
Pisum sativum, Pisum sativum (P47923)
Hammargren, J.; Sundstroem, J.; Johansson, M.; Bergman, P.; Knorpp, C.
On the phylogeny, expression and targeting of plant nucleoside diphosphate kinases
Physiol. Plant.
129
79-89
2007
Arabidopsis thaliana, Pisum sativum (P47922), Pisum sativum (P47923)
Johansson, M.; Hammargren, J.; Uppsaell, E.; MacKenzie, A.; Knorpp, C.
The activities of nucleoside diphosphate kinase and adenylate kinase are influenced by their interaction
Plant Sci.
174
192-199
2008
Pisum sativum
Haque, M.E.; Yoshida, Y.; Hasunuma, K.
ROS resistance in Pisum sativum cv. Alaska: the involvement of nucleoside diphosphate kinase in oxidative stress responses via the regulation of antioxidants
Planta
232
367-382
2010
Pisum sativum, Pisum sativum (C0STY5), Pisum sativum (C0STY7), Pisum sativum (C0STY8)
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