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Protein

Nucleoside diphosphate kinase, cytosolic

Gene

ndkC-1

more
Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Major role in the synthesis of nucleoside triphosphates other than ATP.

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei16 – 161ATP
Binding sitei64 – 641ATP
Binding sitei92 – 921ATP
Binding sitei98 – 981ATP
Binding sitei109 – 1091ATP
Binding sitei119 – 1191ATP
Active sitei122 – 1221Pros-phosphohistidine intermediate

GO - Molecular functioni

  • ATP binding Source: dictyBase
  • metal ion binding Source: UniProtKB-KW
  • nucleoside diphosphate kinase activity Source: dictyBase

GO - Biological processi

  • actin cytoskeleton organization Source: dictyBase
  • cell growth Source: dictyBase
  • CTP biosynthetic process Source: InterPro
  • dGDP phosphorylation Source: dictyBase
  • dGTP biosynthetic process from dGDP Source: dictyBase
  • G-protein coupled receptor signaling pathway Source: dictyBase
  • GTP biosynthetic process Source: InterPro
  • negative regulation of exocytosis Source: dictyBase
  • negative regulation of phagocytosis Source: dictyBase
  • negative regulation of pinocytosis Source: dictyBase
  • nucleoside triphosphate biosynthetic process Source: dictyBase
  • pyrimidine nucleotide metabolic process Source: GO_Central
  • response to bacterium Source: dictyBase
  • translational elongation Source: dictyBase
  • UTP biosynthetic process Source: InterPro
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BRENDAi2.7.4.6. 1939.

Names & Taxonomyi

Protein namesi
Recommended name:
Nucleoside diphosphate kinase, cytosolic (EC:2.7.4.6)
Short name:
NDK
Short name:
NDP kinase
Gene namesi
Name:ndkC-1
Synonyms:gip17, ndkB
ORF Names:DDB_G0273069
AND
Name:ndkC-2
Synonyms:gip17, ndkB
ORF Names:DDB_G0273805
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195 Componentsi: Chromosome 2, Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0273069. ndkC-1.
DDB_G0273805. ndkC-2.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: dictyBase
  • cytoskeleton Source: dictyBase
  • cytosol Source: GO_Central
  • mitochondrion Source: GO_Central
  • phagocytic vesicle Source: dictyBase
  • plasma membrane Source: dictyBase
  • ribosome Source: dictyBase
  • secretory granule Source: dictyBase
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 155155Nucleoside diphosphate kinase, cytosolicPRO_0000137107Add
BLAST

Keywords - PTMi

Phosphoprotein

Proteomic databases

PRIDEiP22887.

2D gel databases

SWISS-2DPAGEP22887.

Interactioni

Subunit structurei

Homohexamer.

Protein-protein interaction databases

STRINGi44689.DDB_0185051.

Structurei

Secondary structure

1
155
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi6 – 83Combined sources
Beta strandi10 – 156Combined sources
Helixi17 – 215Combined sources
Helixi25 – 3511Combined sources
Beta strandi38 – 458Combined sources
Helixi49 – 557Combined sources
Helixi57 – 593Combined sources
Beta strandi60 – 623Combined sources
Helixi65 – 728Combined sources
Beta strandi77 – 848Combined sources
Helixi87 – 959Combined sources
Helixi100 – 1023Combined sources
Helixi108 – 1125Combined sources
Beta strandi116 – 1183Combined sources
Beta strandi121 – 1233Combined sources
Helixi127 – 13711Combined sources
Helixi140 – 1423Combined sources
Turni151 – 1533Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B4SX-ray2.50A/B/C1-155[»]
1B99X-ray2.70A/B/C/D/E/F1-155[»]
1BUXX-ray2.80A/B/C1-155[»]
1F3FX-ray1.85A/B/C1-155[»]
1F6TX-ray1.92A/B/C1-155[»]
1HHQX-ray2.10A1-155[»]
1HIYX-ray2.60A/B/C1-155[»]
1HLWX-ray1.90A1-155[»]
1KDNX-ray2.00A/B/C1-155[»]
1LEOX-ray2.60A6-155[»]
1LWXX-ray2.30A/B/C1-155[»]
1MN7X-ray2.15A/B1-155[»]
1MN9X-ray2.90A/B/C1-155[»]
1NCLX-ray2.20A6-155[»]
1NDCX-ray2.00A1-155[»]
1NDKX-ray2.20A1-155[»]
1NDPX-ray2.20A/B1-155[»]
1NPKX-ray1.80A2-155[»]
1NSPX-ray2.10A1-155[»]
1PAEX-ray2.70X1-155[»]
1S5ZX-ray2.00A/B/C/D/E/F1-155[»]
2BEFX-ray2.30A/B/C1-155[»]
3FKBX-ray1.65A/B/C/D/E/F1-155[»]
4C6AX-ray1.25A2-155[»]
4CP5X-ray2.32A/B/C/D/E/F1-155[»]
ProteinModelPortaliP22887.
SMRiP22887. Positions 5-155.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22887.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiCOG0105.
InParanoidiP22887.
KOiK00940.
OMAiASKRIHM.
PhylomeDBiP22887.

Family and domain databases

Gene3Di3.30.70.141. 1 hit.
HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
SUPFAMiSSF54919. SSF54919. 1 hit.
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P22887-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSTNKVNKER TFLAVKPDGV ARGLVGEIIA RYEKKGFVLV GLKQLVPTKD
60 70 80 90 100
LAESHYAEHK ERPFFGGLVS FITSGPVVAM VFEGKGVVAS ARLMIGVTNP
110 120 130 140 150
LASAPGSIRG DFGVDVGRNI IHGSDSVESA NREIALWFKP EELLTEVKPN

PNLYE
Length:155
Mass (Da):16,794
Last modified:August 1, 1991 - v1
Checksum:i426DB78B1AF2307A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05457 mRNA. Translation: AAA33231.1.
L23067 Genomic DNA. Translation: AAA16161.1.
AAFI02000011 Genomic DNA. Translation: EAL70593.1.
AAFI02000009 Genomic DNA. Translation: EAL70752.1.
PIRiA49547.
RefSeqiXP_644519.1. XM_639427.1.
XP_644731.1. XM_639639.1.

Genome annotation databases

EnsemblProtistsiDDB0185051; DDB0185051; DDB_G0273069.
DDB0238334; DDB0238334; DDB_G0273805.
GeneIDi8618831.
8619145.
KEGGiddi:DDB_G0273069.
ddi:DDB_G0273805.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
J05457 mRNA. Translation: AAA33231.1.
L23067 Genomic DNA. Translation: AAA16161.1.
AAFI02000011 Genomic DNA. Translation: EAL70593.1.
AAFI02000009 Genomic DNA. Translation: EAL70752.1.
PIRiA49547.
RefSeqiXP_644519.1. XM_639427.1.
XP_644731.1. XM_639639.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1B4SX-ray2.50A/B/C1-155[»]
1B99X-ray2.70A/B/C/D/E/F1-155[»]
1BUXX-ray2.80A/B/C1-155[»]
1F3FX-ray1.85A/B/C1-155[»]
1F6TX-ray1.92A/B/C1-155[»]
1HHQX-ray2.10A1-155[»]
1HIYX-ray2.60A/B/C1-155[»]
1HLWX-ray1.90A1-155[»]
1KDNX-ray2.00A/B/C1-155[»]
1LEOX-ray2.60A6-155[»]
1LWXX-ray2.30A/B/C1-155[»]
1MN7X-ray2.15A/B1-155[»]
1MN9X-ray2.90A/B/C1-155[»]
1NCLX-ray2.20A6-155[»]
1NDCX-ray2.00A1-155[»]
1NDKX-ray2.20A1-155[»]
1NDPX-ray2.20A/B1-155[»]
1NPKX-ray1.80A2-155[»]
1NSPX-ray2.10A1-155[»]
1PAEX-ray2.70X1-155[»]
1S5ZX-ray2.00A/B/C/D/E/F1-155[»]
2BEFX-ray2.30A/B/C1-155[»]
3FKBX-ray1.65A/B/C/D/E/F1-155[»]
4C6AX-ray1.25A2-155[»]
4CP5X-ray2.32A/B/C/D/E/F1-155[»]
ProteinModelPortaliP22887.
SMRiP22887. Positions 5-155.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi44689.DDB_0185051.

2D gel databases

SWISS-2DPAGEP22887.

Proteomic databases

PRIDEiP22887.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsiDDB0185051; DDB0185051; DDB_G0273069.
DDB0238334; DDB0238334; DDB_G0273805.
GeneIDi8618831.
8619145.
KEGGiddi:DDB_G0273069.
ddi:DDB_G0273805.

Organism-specific databases

dictyBaseiDDB_G0273069. ndkC-1.
DDB_G0273805. ndkC-2.

Phylogenomic databases

eggNOGiCOG0105.
InParanoidiP22887.
KOiK00940.
OMAiASKRIHM.
PhylomeDBiP22887.

Enzyme and pathway databases

BRENDAi2.7.4.6. 1939.

Miscellaneous databases

EvolutionaryTraceiP22887.
PROiP22887.

Family and domain databases

Gene3Di3.30.70.141. 1 hit.
HAMAPiMF_00451. NDP_kinase.
InterProiIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamiPF00334. NDK. 1 hit.
[Graphical view]
PRINTSiPR01243. NUCDPKINASE.
SMARTiSM00562. NDK. 1 hit.
[Graphical view]
SUPFAMiSSF54919. SSF54919. 1 hit.
PROSITEiPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Functional cloning of a nucleoside diphosphate kinase from Dictyostelium discoideum."
    Lacombe M.-L., Wallet V., Troll H., Veron M.
    J. Biol. Chem. 265:10012-10018(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "Separate nuclear genes encode cytosolic and mitochondrial nucleoside diphosphate kinase in Dictyostelium discoideum."
    Troll H., Winckler T., Lascu I., Mueller N., Saurin W., Veron M., Mutzel R.
    J. Biol. Chem. 268:25469-25475(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: AX2.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.
  4. "The genome of the social amoeba Dictyostelium discoideum."
    Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N.
    , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.
    Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: AX4.
  5. "Proteomics fingerprinting of phagosome maturation and evidence for the role of a Galpha during uptake."
    Gotthardt D., Blancheteau V., Bosserhoff A., Ruppert T., Delorenzi M., Soldati T.
    Mol. Cell. Proteomics 5:2228-2243(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Strain: AX2.
  6. "X-ray structure of nucleoside diphosphate kinase."
    Dumas C., Lascu I., Morera S., Glaser P., Fourme R., Wallet V., Lacombe M.-L., Veron M., Janin J.
    EMBO J. 11:3203-3208(1992) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
  7. "Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate kinase at 1.8-A resolution."
    Morera S., Lebras G., Lascu I., Lacombe M.-L., Veron M., Janin J.
    J. Mol. Biol. 243:873-890(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
  8. "Nucleoside diphosphate kinase. Investigation of the intersubunit contacts by site-directed mutagenesis and crystallography."
    Karlsson A., Mesnildrey S., Xu Y., Morera S., Janin J., Veron M.
    J. Biol. Chem. 271:19928-19934(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
  9. "X-ray analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase."
    Xu Y., Sellam O., Morera S., Sarfati S., Biondi R., Veron M., Janin J.
    Proc. Natl. Acad. Sci. U.S.A. 94:7162-7165(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
  10. "3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity."
    Schneider B., Xu Y.W., Janin J., Veron M., Deville-Bonne D.
    J. Biol. Chem. 273:28773-28778(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
  11. "Nucleophilic activation by positioning in phosphoryl transfer catalyzed by nucleoside diphosphate kinase."
    Admiraal S.J., Schneider B., Meyer P., Janin J., Veron M., Deville-Bonne D., Herschlag D.
    Biochemistry 38:4701-4711(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
  12. "Catalytic mechanism of nucleoside diphosphate kinase investigated using nucleotide analogues, viscosity effects, and X-ray crystallography."
    Gonin P., Xu Y., Milon L., Dabernat S., Morr M., Kumar R., Lacombe M.L., Janin J., Lascu I.
    Biochemistry 38:7265-7272(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).

Entry informationi

Entry nameiNDKC_DICDI
AccessioniPrimary (citable) accession number: P22887
Secondary accession number(s): Q556V0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: May 27, 2015
This is version 138 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Caution

The gene for this protein is duplicated in strains AX3 and AX4. These strains contain a duplication of a segment of 750 kb of chromosome 2 compared to the corresponding sequence in strain AX2.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.