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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)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
  • 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
  • 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 lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
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.

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.
OMAiAEHSERP.
PhylomeDBiP22887.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
InterProiView protein in InterPro
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.
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.

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
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...

Protein-protein interaction databases

STRINGi44689.DDB0238334.

2D gel databases

SWISS-2DPAGEP22887.

Proteomic databases

PaxDbiP22887.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

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

Phylogenomic databases

eggNOGiKOG0888. Eukaryota.
COG0105. LUCA.
InParanoidiP22887.
KOiK00940.
OMAiAEHSERP.
PhylomeDBiP22887.

Enzyme and pathway databases

BRENDAi2.7.4.6. 1939.

Miscellaneous databases

EvolutionaryTraceiP22887.
PROiP22887.

Family and domain databases

HAMAPiMF_00451. NDP_kinase. 1 hit.
InterProiView protein in InterPro
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.
PROSITEiView protein in PROSITE
PS00469. NDP_KINASES. 1 hit.
ProtoNetiSearch...

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: March 15, 2017
This is version 151 of the entry and version 1 of the sequence. See 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

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 one 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.