P22887 (NDKC_DICDI) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Dictyostelium discoideum (Slime mold) [Reference proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	155 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Major role in the synthesis of nucleoside triphosphates other than ATP.
Catalytic activity	ATP + nucleoside diphosphate = ADP + nucleoside triphosphate.
Cofactor	Magnesium By similarity.
Subunit structure	Homohexamer.
Subcellular location	Cytoplasm.
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 process	Nucleotide metabolism
Cellular component	Cytoplasm
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Kinase Transferase
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	CTP 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 response to bacterium Inferred from expression pattern PubMed 19482547. Source: dictyBase translational elongation Inferred from direct assay PubMed 7733916. Source: dictyBase
Cellular_component	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_function	ATP 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 key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 155

155

Nucleoside diphosphate kinase, cytosolic

PRO_0000137107

Sites

Active site

122

1

Pros-phosphohistidine intermediate

Binding site

16

1

ATP

Binding site

64

1

ATP

Binding site

92

1

ATP

Binding site

98

1

ATP

Binding site

109

1

ATP

Binding site

119

1

ATP

Secondary structure

1

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155

Helix Strand Turn

Details...

Beta strand

10 – 15

6

Helix

17 – 21

5

Helix

25 – 35

11

Beta strand

38 – 45

8

Helix

49 – 55

7

Helix

57 – 59

3

Beta strand

60 – 62

3

Helix

65 – 72

8

Beta strand

77 – 84

8

Helix

87 – 95

9

Helix

100 – 102

3

Helix

108 – 112

5

Beta strand

116 – 118

3

Beta strand

120 – 123

4

Helix

127 – 137

11

Helix

140 – 142

3

Turn

151 – 153

3

Sequences

	Sequence		Length	Mass (Da)
	P22887 [UniParc]. Last modified August 1, 1991. Version 1. Checksum: 426DB78B1AF2307A	FASTA	155	16,794
	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

References

	« Hide 'large scale' referencesShow '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. , 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.

PIR

A49547.

RefSeq

XP_644519.1. XM_639427.1.
XP_644731.1. XM_639639.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

ProteinModelPortal

P22887.

SMR

P22887. Positions 5-155.

ModBase

Search...

Protein-protein interaction databases

STRING

44689.DDB_0185051.

2D gel databases

SWISS-2DPAGE

P22887.

Proteomic databases

PRIDE

P22887.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblProtists

DDB0185051; DDB0185051; DDB_G0273069.
DDB0238334; DDB0238334; DDB_G0273805.

GeneID

8618831.
8619145.

KEGG

ddi:DDB_G0273069.
ddi:DDB_G0273805.

Organism-specific databases

dictyBase

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

Phylogenomic databases

eggNOG

COG0105.

KO

K00940.

OMA

DERTFIM.

ProtClustDB

PTZ00093.

Family and domain databases

Gene3D

3.30.70.141. 1 hit.

InterPro

IPR001564. Nucleoside_diP_kinase.
IPR023005. Nucleoside_diP_kinase_AS.
[Graphical view]

PANTHER

PTHR11349. PTHR11349. 1 hit.

Pfam

PF00334. NDK. 1 hit.
[Graphical view]

PRINTS

PR01243. NUCDPKINASE.

SMART

SM00562. NDK. 1 hit.
[Graphical view]

SUPFAM

SSF54919. NDK. 1 hit.

PROSITE

PS00469. NDP_KINASES. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P22887.

Entry information

Entry name

NDKC_DICDI

Accession

Primary (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:	May 1, 2013
This is version 123 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)