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Protein

Nucleoside diphosphate kinase, cytosolic

Gene

ndkC-1

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

Functioni

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

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

Catalytic activityi

ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei16ATP1
Binding sitei64ATP1
Binding sitei92ATP1
Binding sitei98ATP1
Binding sitei109ATP1
Binding sitei119ATP1
Active sitei122Pros-phosphohistidine intermediate1

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
  • asexual reproduction 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
  • response to bacterium Source: dictyBase
  • translational elongation Source: dictyBase
  • UTP biosynthetic process Source: InterPro

Keywordsi

Molecular functionKinase, Transferase
Biological processNucleotide metabolism
LigandATP-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 lineageiEukaryotaAmoebozoaMycetozoaDictyostelidsDictyostelialesDictyosteliaceaeDictyostelium
Proteomesi
  • UP000002195 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
  • phagocytic vesicle Source: dictyBase
  • plasma membrane Source: dictyBase
  • ribosome Source: dictyBase
  • secretory granule Source: dictyBase

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001371071 – 155Nucleoside diphosphate kinase, cytosolicAdd BLAST155

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiP22887
PRIDEiP22887

2D gel databases

SWISS-2DPAGEP22887

Interactioni

Subunit structurei

Homohexamer.

Protein-protein interaction databases

STRINGi44689.DDB0238334

Structurei

Secondary structure

1155
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi6 – 8Combined sources3
Beta strandi10 – 15Combined sources6
Helixi17 – 21Combined sources5
Helixi25 – 35Combined sources11
Beta strandi38 – 45Combined sources8
Helixi49 – 55Combined sources7
Helixi57 – 59Combined sources3
Beta strandi60 – 62Combined sources3
Helixi65 – 72Combined sources8
Beta strandi77 – 84Combined sources8
Helixi87 – 95Combined sources9
Helixi100 – 102Combined sources3
Helixi108 – 112Combined sources5
Beta strandi116 – 118Combined sources3
Beta strandi121 – 123Combined sources3
Helixi127 – 137Combined sources11
Helixi140 – 142Combined sources3
Turni151 – 153Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB 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
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP22887

Family & Domainsi

Sequence similaritiesi

Belongs to the NDK family.Curated

Phylogenomic databases

eggNOGiKOG0888 Eukaryota
COG0105 LUCA
InParanoidiP22887
KOiK00940
OMAiRLVKYMG
PhylomeDBiP22887

Family and domain databases

Gene3Di3.30.70.141, 1 hit
HAMAPiMF_00451 NDP_kinase, 1 hit
InterProiView protein in InterPro
IPR034907 NDK-like_dom
IPR036850 NDK-like_dom_sf
IPR001564 Nucleoside_diP_kinase
IPR023005 Nucleoside_diP_kinase_AS
PfamiView protein in Pfam
PF00334 NDK, 1 hit
PRINTSiPR01243 NUCDPKINASE
SMARTiView protein in SMART
SM00562 NDK, 1 hit
SUPFAMiSSF54919 SSF54919, 1 hit
PROSITEiView protein in PROSITE
PS00469 NDP_KINASES, 1 hit

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

EnsemblProtistsiEAL70593; EAL70593; DDB_G0273805
EAL70752; EAL70752; DDB_G0273069
GeneIDi8618831
8619145
KEGGiddi:DDB_G0273069
ddi:DDB_G0273805

Similar proteinsi

Entry informationi

Entry nameiNDKC_DICDI
AccessioniPrimary (citable) accession number: P22887
Secondary accession number(s): Q556V0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1991
Last sequence update: August 1, 1991
Last modified: May 23, 2018
This is version 160 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

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