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P22887

- NDKC_DICDI

UniProt

P22887 - NDKC_DICDI

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Protein
Nucleoside diphosphate kinase, cytosolic
Gene
ndkC-1, gip17, ndkB, DDB_G0273069
ndkC-2, gip17, ndkB, DDB_G0273805
Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

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

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.UniRule annotation

Cofactori

Magnesium By similarity.UniRule annotation

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

  1. ATP binding Source: dictyBase
  2. metal ion binding Source: UniProtKB-KW
  3. nucleoside diphosphate kinase activity Source: dictyBase

GO - Biological processi

  1. CTP biosynthetic process Source: InterPro
  2. G-protein coupled receptor signaling pathway Source: dictyBase
  3. GTP biosynthetic process Source: InterPro
  4. UTP biosynthetic process Source: InterPro
  5. actin cytoskeleton organization Source: dictyBase
  6. cell growth Source: dictyBase
  7. dGDP phosphorylation Source: dictyBase
  8. dGTP biosynthetic process from dGDP Source: dictyBase
  9. negative regulation of exocytosis Source: dictyBase
  10. negative regulation of phagocytosis Source: dictyBase
  11. negative regulation of pinocytosis Source: dictyBase
  12. nucleoside triphosphate biosynthetic process Source: dictyBase
  13. response to bacterium Source: dictyBase
  14. translational elongation Source: dictyBase
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Biological processi

Nucleotide metabolism

Keywords - Ligandi

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

Names & Taxonomyi

Organism-specific databases

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: Chromosome 2, UP000002195: Unassembled WGS sequence
dictyBaseiDDB_G0273069. ndkC-1.
DDB_G0273805. ndkC-2.

Subcellular locationi

Cytoplasm UniRule annotation

GO - Cellular componenti

  1. cytoplasm Source: dictyBase
  2. cytoskeleton Source: dictyBase
  3. phagocytic vesicle Source: dictyBase
  4. plasma membrane Source: dictyBase
  5. ribosome Source: dictyBase
  6. secretory granule Source: dictyBase

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 155155Nucleoside diphosphate kinase, cytosolicUniRule annotation
PRO_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

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

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
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[»]
ProteinModelPortaliP22887.
SMRiP22887. Positions 5-155.

Miscellaneous databases

EvolutionaryTraceiP22887.

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.

Phylogenomic databases

eggNOGiCOG0105.
KOiK00940.
OMAiGGENWIS.
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

MSTNKVNKER TFLAVKPDGV ARGLVGEIIA RYEKKGFVLV GLKQLVPTKD    50
LAESHYAEHK ERPFFGGLVS FITSGPVVAM VFEGKGVVAS ARLMIGVTNP 100
LASAPGSIRG DFGVDVGRNI IHGSDSVESA NREIALWFKP EELLTEVKPN 150
PNLYE 155
Length:155
Mass (Da):16,794
Last modified:August 1, 1991 - v1
Checksum:i426DB78B1AF2307A
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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:
EMBL
GenBank
DDBJ
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 .
PIRi A49547.
RefSeqi XP_644519.1. XM_639427.1.
XP_644731.1. XM_639639.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1B4S X-ray 2.50 A/B/C 1-155 [» ]
1B99 X-ray 2.70 A/B/C/D/E/F 1-155 [» ]
1BUX X-ray 2.80 A/B/C 1-155 [» ]
1F3F X-ray 1.85 A/B/C 1-155 [» ]
1F6T X-ray 1.92 A/B/C 1-155 [» ]
1HHQ X-ray 2.10 A 1-155 [» ]
1HIY X-ray 2.60 A/B/C 1-155 [» ]
1HLW X-ray 1.90 A 1-155 [» ]
1KDN X-ray 2.00 A/B/C 1-155 [» ]
1LEO X-ray 2.60 A 6-155 [» ]
1LWX X-ray 2.30 A/B/C 1-155 [» ]
1MN7 X-ray 2.15 A/B 1-155 [» ]
1MN9 X-ray 2.90 A/B/C 1-155 [» ]
1NCL X-ray 2.20 A 6-155 [» ]
1NDC X-ray 2.00 A 1-155 [» ]
1NDK X-ray 2.20 A 1-155 [» ]
1NDP X-ray 2.20 A/B 1-155 [» ]
1NPK X-ray 1.80 A 2-155 [» ]
1NSP X-ray 2.10 A 1-155 [» ]
1PAE X-ray 2.70 X 1-155 [» ]
1S5Z X-ray 2.00 A/B/C/D/E/F 1-155 [» ]
2BEF X-ray 2.30 A/B/C 1-155 [» ]
3FKB X-ray 1.65 A/B/C/D/E/F 1-155 [» ]
4C6A X-ray 1.25 A 2-155 [» ]
ProteinModelPortali P22887.
SMRi P22887. Positions 5-155.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 44689.DDB_0185051.

2D gel databases

SWISS-2DPAGE P22887.

Proteomic databases

PRIDEi P22887.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblProtistsi DDB0185051 ; DDB0185051 ; DDB_G0273069 .
DDB0238334 ; DDB0238334 ; DDB_G0273805 .
GeneIDi 8618831.
8619145.
KEGGi ddi:DDB_G0273069.
ddi:DDB_G0273805.

Organism-specific databases

dictyBasei DDB_G0273069. ndkC-1.
DDB_G0273805. ndkC-2.

Phylogenomic databases

eggNOGi COG0105.
KOi K00940.
OMAi GGENWIS.
PhylomeDBi P22887.

Miscellaneous databases

EvolutionaryTracei P22887.

Family and domain databases

Gene3Di 3.30.70.141. 1 hit.
HAMAPi MF_00451. NDP_kinase.
InterProi IPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view ]
Pfami PF00334. NDK. 1 hit.
[Graphical view ]
PRINTSi PR01243. NUCDPKINASE.
SMARTi SM00562. NDK. 1 hit.
[Graphical view ]
SUPFAMi SSF54919. SSF54919. 1 hit.
PROSITEi PS00469. NDP_KINASES. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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: September 3, 2014
This is version 130 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.

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

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