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P22887 (NDKC_DICDI) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Nucleoside diphosphate kinase, cytosolic

Short name=NDK
Short name=NDP kinase
EC=2.7.4.6
Gene names
Name:ndkC-1
Synonyms:gip17, ndkB
ORF Names:DDB_G0273069
AND
Name:ndkC-2
Synonyms:gip17, ndkB
ORF Names:DDB_G0273805
OrganismDictyostelium discoideum (Slime mold) [Reference proteome]
Taxonomic identifier44689 [NCBI]
Taxonomic lineageEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium

Protein attributes

Sequence length155 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Major role in the synthesis of nucleoside triphosphates other than ATP. HAMAP-Rule MF_00451

Catalytic activity

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate. HAMAP-Rule MF_00451

Cofactor

Magnesium By similarity. HAMAP-Rule MF_00451

Subunit structure

Homohexamer.

Subcellular location

Cytoplasm HAMAP-Rule MF_00451.

Sequence similarities

Belongs to the NDK family.

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.

Ontologies

Keywords
   Biological processNucleotide metabolism
   Cellular componentCytoplasm
   LigandATP-binding
Magnesium
Metal-binding
Nucleotide-binding
   Molecular functionKinase
Transferase
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processCTP biosynthetic process

Inferred from electronic annotation. Source: InterPro

G-protein coupled receptor signaling pathway

Inferred from mutant phenotype PubMed 8389692. Source: dictyBase

GTP biosynthetic process

Inferred from electronic annotation. Source: InterPro

UTP biosynthetic process

Inferred from electronic annotation. Source: InterPro

actin cytoskeleton organization

Inferred from direct assay PubMed 8816286. Source: dictyBase

cell growth

Inferred from mutant phenotype PubMed 21991393. Source: dictyBase

dGDP phosphorylation

Inferred from direct assay Ref.1. Source: dictyBase

dGTP biosynthetic process from dGDP

Inferred from direct assay Ref.1. Source: dictyBase

negative regulation of exocytosis

Inferred from mutant phenotype PubMed 21991393. Source: dictyBase

negative regulation of phagocytosis

Inferred from mutant phenotype PubMed 21991393. Source: dictyBase

negative regulation of pinocytosis

Inferred from mutant phenotype PubMed 21991393. Source: dictyBase

nucleoside triphosphate biosynthetic process

Inferred from direct assay Ref.1. Source: dictyBase

response to bacterium

Inferred from expression pattern PubMed 19482547. Source: dictyBase

translational elongation

Inferred from direct assay PubMed 7733916. Source: dictyBase

   Cellular_componentcytoplasm

Inferred from direct assay PubMed 21991393Ref.2. Source: dictyBase

cytoskeleton

Inferred from direct assay PubMed 8816286. Source: dictyBase

phagocytic vesicle

Inferred from direct assay Ref.5PubMed 19482547. Source: dictyBase

plasma membrane

Inferred from direct assay PubMed 8389692. Source: dictyBase

ribosome

Inferred from direct assay PubMed 7733916. Source: dictyBase

secretory granule

Inferred from direct assay PubMed 11990506. Source: dictyBase

   Molecular_functionATP binding

Inferred from direct assay Ref.1. Source: dictyBase

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

nucleoside diphosphate kinase activity

Inferred from direct assay Ref.1. Source: dictyBase

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 155155Nucleoside diphosphate kinase, cytosolic HAMAP-Rule MF_00451
PRO_0000137107

Sites

Active site1221Pros-phosphohistidine intermediate
Binding site161ATP
Binding site641ATP
Binding site921ATP
Binding site981ATP
Binding site1091ATP
Binding site1191ATP

Secondary structure

.................................... 155
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P22887 [UniParc].

Last modified August 1, 1991. Version 1.
Checksum: 426DB78B1AF2307A

FASTA15516,794
        10         20         30         40         50         60 
MSTNKVNKER TFLAVKPDGV ARGLVGEIIA RYEKKGFVLV GLKQLVPTKD LAESHYAEHK 

        70         80         90        100        110        120 
ERPFFGGLVS FITSGPVVAM VFEGKGVVAS ARLMIGVTNP LASAPGSIRG DFGVDVGRNI 

       130        140        150 
IHGSDSVESA NREIALWFKP EELLTEVKPN PNLYE 

« Hide

References

« Hide 'large scale' references
[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]"Sequence and analysis of chromosome 2 of Dictyostelium discoideum."
Gloeckner G., Eichinger L., Szafranski K., Pachebat J.A., Bankier A.T., Dear P.H., Lehmann R., Baumgart C., Parra G., Abril J.F., Guigo R., Kumpf K., Tunggal B., Cox E.C., Quail M.A., Platzer M., Rosenthal A., Noegel A.A.
Nature 418:79-85(2002) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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).
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
J05457 mRNA. Translation: AAA33231.1.
L23067 Genomic DNA. Translation: AAA16161.1.
AAFI02000011 Genomic DNA. Translation: EAL70593.1.
AAFI02000009 Genomic DNA. Translation: EAL70752.1.
PIRA49547.
RefSeqXP_644519.1. XM_639427.1.
XP_644731.1. XM_639639.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
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[»]
ProteinModelPortalP22887.
SMRP22887. Positions 5-155.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING44689.DDB_0185051.

2D gel databases

SWISS-2DPAGEP22887.

Proteomic databases

PRIDEP22887.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblProtistsDDB0185051; DDB0185051; DDB_G0273069.
DDB0238334; DDB0238334; DDB_G0273805.
GeneID8618831.
8619145.
KEGGddi:DDB_G0273069.
ddi:DDB_G0273805.

Organism-specific databases

dictyBaseDDB_G0273069. ndkC-1.
DDB_G0273805. ndkC-2.

Phylogenomic databases

eggNOGCOG0105.
OMAGGENWIS.
PhylomeDBP22887.

Family and domain databases

Gene3D3.30.70.141. 1 hit.
HAMAPMF_00451. NDP_kinase.
InterProIPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]
PfamPF00334. NDK. 1 hit.
[Graphical view]
PRINTSPR01243. NUCDPKINASE.
SMARTSM00562. NDK. 1 hit.
[Graphical view]
SUPFAMSSF54919. SSF54919. 1 hit.
PROSITEPS00469. NDP_KINASES. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP22887.

Entry information

Entry nameNDKC_DICDI
AccessionPrimary (citable) accession number: P22887
Secondary accession number(s): Q556V0
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: July 9, 2014
This is version 129 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Dictyostelium discoideum

Dictyostelium discoideum: entries, gene names and cross-references to dictyBase