NDKC_DICDI
ID NDKC_DICDI Reviewed; 155 AA.
AC P22887; Q556V0;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1991, sequence version 1.
DT 03-AUG-2022, entry version 176.
DE RecName: Full=Nucleoside diphosphate kinase, cytosolic;
DE Short=NDK;
DE Short=NDP kinase;
DE EC=2.7.4.6;
GN Name=ndkC-1; Synonyms=gip17, ndkB; ORFNames=DDB_G0273069;
GN and
GN Name=ndkC-2; Synonyms=gip17, ndkB; ORFNames=DDB_G0273805;
OS Dictyostelium discoideum (Slime mold).
OC Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC Dictyosteliaceae; Dictyostelium.
OX NCBI_TaxID=44689;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=2161830; DOI=10.1016/s0021-9258(19)38771-x;
RA Lacombe M.-L., Wallet V., Troll H., Veron M.;
RT "Functional cloning of a nucleoside diphosphate kinase from Dictyostelium
RT discoideum.";
RL J. Biol. Chem. 265:10012-10018(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=AX2;
RX PubMed=8244981; DOI=10.1016/s0021-9258(19)74415-9;
RA Troll H., Winckler T., Lascu I., Mueller N., Saurin W., Veron M.,
RA Mutzel R.;
RT "Separate nuclear genes encode cytosolic and mitochondrial nucleoside
RT diphosphate kinase in Dictyostelium discoideum.";
RL J. Biol. Chem. 268:25469-25475(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=12097910; DOI=10.1038/nature00847;
RA Gloeckner G., Eichinger L., Szafranski K., Pachebat J.A., Bankier A.T.,
RA Dear P.H., Lehmann R., Baumgart C., Parra G., Abril J.F., Guigo R.,
RA Kumpf K., Tunggal B., Cox E.C., Quail M.A., Platzer M., Rosenthal A.,
RA Noegel A.A.;
RT "Sequence and analysis of chromosome 2 of Dictyostelium discoideum.";
RL Nature 418:79-85(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AX4;
RX PubMed=15875012; DOI=10.1038/nature03481;
RA Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT "The genome of the social amoeba Dictyostelium discoideum.";
RL Nature 435:43-57(2005).
RN [5]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=AX2;
RX PubMed=16926386; DOI=10.1074/mcp.m600113-mcp200;
RA Gotthardt D., Blancheteau V., Bosserhoff A., Ruppert T., Delorenzi M.,
RA Soldati T.;
RT "Proteomics fingerprinting of phagosome maturation and evidence for the
RT role of a Galpha during uptake.";
RL Mol. Cell. Proteomics 5:2228-2243(2006).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
RX PubMed=1324167; DOI=10.1002/j.1460-2075.1992.tb05397.x;
RA Dumas C., Lascu I., Morera S., Glaser P., Fourme R., Wallet V.,
RA Lacombe M.-L., Veron M., Janin J.;
RT "X-ray structure of nucleoside diphosphate kinase.";
RL EMBO J. 11:3203-3208(1992).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
RX PubMed=7966307; DOI=10.1006/jmbi.1994.1689;
RA Morera S., Lebras G., Lascu I., Lacombe M.-L., Veron M., Janin J.;
RT "Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate
RT kinase at 1.8-A resolution.";
RL J. Mol. Biol. 243:873-890(1994).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS).
RX PubMed=8702707; DOI=10.1074/jbc.271.33.19928;
RA Karlsson A., Mesnildrey S., Xu Y., Morera S., Janin J., Veron M.;
RT "Nucleoside diphosphate kinase. Investigation of the intersubunit contacts
RT by site-directed mutagenesis and crystallography.";
RL J. Biol. Chem. 271:19928-19934(1996).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
RX PubMed=9207061; DOI=10.1073/pnas.94.14.7162;
RA Xu Y., Sellam O., Morera S., Sarfati S., Biondi R., Veron M., Janin J.;
RT "X-ray analysis of azido-thymidine diphosphate binding to nucleoside
RT diphosphate kinase.";
RL Proc. Natl. Acad. Sci. U.S.A. 94:7162-7165(1997).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS).
RX PubMed=9786875; DOI=10.1074/jbc.273.44.28773;
RA Schneider B., Xu Y.W., Janin J., Veron M., Deville-Bonne D.;
RT "3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside
RT diphosphate kinase activity.";
RL J. Biol. Chem. 273:28773-28778(1998).
RN [11]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RX PubMed=10200157; DOI=10.1021/bi9827565;
RA Admiraal S.J., Schneider B., Meyer P., Janin J., Veron M.,
RA Deville-Bonne D., Herschlag D.;
RT "Nucleophilic activation by positioning in phosphoryl transfer catalyzed by
RT nucleoside diphosphate kinase.";
RL Biochemistry 38:4701-4711(1999).
RN [12]
RP X-RAY CRYSTALLOGRAPHY (2.7 ANGSTROMS).
RX PubMed=10353838; DOI=10.1021/bi982990v;
RA Gonin P., Xu Y., Milon L., Dabernat S., Morr M., Kumar R., Lacombe M.L.,
RA Janin J., Lascu I.;
RT "Catalytic mechanism of nucleoside diphosphate kinase investigated using
RT nucleotide analogues, viscosity effects, and X-ray crystallography.";
RL Biochemistry 38:7265-7272(1999).
CC -!- FUNCTION: Major role in the synthesis of nucleoside triphosphates other
CC than ATP.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a 2'-deoxyribonucleoside 5'-diphosphate + ATP = a 2'-
CC deoxyribonucleoside 5'-triphosphate + ADP; Xref=Rhea:RHEA:44640,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:61560, ChEBI:CHEBI:73316,
CC ChEBI:CHEBI:456216; EC=2.7.4.6;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a ribonucleoside 5'-diphosphate + ATP = a ribonucleoside 5'-
CC triphosphate + ADP; Xref=Rhea:RHEA:18113, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:57930, ChEBI:CHEBI:61557, ChEBI:CHEBI:456216; EC=2.7.4.6;
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- SUBUNIT: Homohexamer.
CC -!- SUBCELLULAR LOCATION: Cytoplasm.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000305}.
CC -!- CAUTION: The gene for this protein is duplicated in strains AX3 and
CC AX4. These strains contain a duplication of a segment of 750 kb of
CC chromosome 2 compared to the corresponding sequence in strain AX2.
CC {ECO:0000305}.
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DR EMBL; J05457; AAA33231.1; -; mRNA.
DR EMBL; L23067; AAA16161.1; -; Genomic_DNA.
DR EMBL; AAFI02000011; EAL70593.1; -; Genomic_DNA.
DR EMBL; AAFI02000009; EAL70752.1; -; Genomic_DNA.
DR PIR; A49547; A49547.
DR RefSeq; XP_644519.1; XM_639427.1.
DR RefSeq; XP_644731.1; XM_639639.1.
DR PDB; 1B4S; X-ray; 2.50 A; A/B/C=1-155.
DR PDB; 1B99; X-ray; 2.70 A; A/B/C/D/E/F=1-155.
DR PDB; 1BUX; X-ray; 2.80 A; A/B/C=1-155.
DR PDB; 1F3F; X-ray; 1.85 A; A/B/C=1-155.
DR PDB; 1F6T; X-ray; 1.92 A; A/B/C=1-155.
DR PDB; 1HHQ; X-ray; 2.10 A; A=1-155.
DR PDB; 1HIY; X-ray; 2.60 A; A/B/C=1-155.
DR PDB; 1HLW; X-ray; 1.90 A; A=1-155.
DR PDB; 1KDN; X-ray; 2.00 A; A/B/C=1-155.
DR PDB; 1LEO; X-ray; 2.60 A; A=6-155.
DR PDB; 1LWX; X-ray; 2.30 A; A/B/C=1-155.
DR PDB; 1MN7; X-ray; 2.15 A; A/B=1-155.
DR PDB; 1MN9; X-ray; 2.90 A; A/B/C=1-155.
DR PDB; 1NCL; X-ray; 2.20 A; A=6-155.
DR PDB; 1NDC; X-ray; 2.00 A; A=1-155.
DR PDB; 1NDK; X-ray; 2.20 A; A=1-155.
DR PDB; 1NDP; X-ray; 2.20 A; A/B=1-155.
DR PDB; 1NPK; X-ray; 1.80 A; A=2-155.
DR PDB; 1NSP; X-ray; 2.10 A; A=1-155.
DR PDB; 1PAE; X-ray; 2.70 A; X=1-155.
DR PDB; 1S5Z; X-ray; 2.00 A; A/B/C/D/E/F=1-155.
DR PDB; 2BEF; X-ray; 2.30 A; A/B/C=1-155.
DR PDB; 3FKB; X-ray; 1.65 A; A/B/C/D/E/F=1-155.
DR PDB; 4C6A; X-ray; 1.25 A; A=2-155.
DR PDB; 4CP5; X-ray; 2.32 A; A/B/C/D/E/F=1-155.
DR PDBsum; 1B4S; -.
DR PDBsum; 1B99; -.
DR PDBsum; 1BUX; -.
DR PDBsum; 1F3F; -.
DR PDBsum; 1F6T; -.
DR PDBsum; 1HHQ; -.
DR PDBsum; 1HIY; -.
DR PDBsum; 1HLW; -.
DR PDBsum; 1KDN; -.
DR PDBsum; 1LEO; -.
DR PDBsum; 1LWX; -.
DR PDBsum; 1MN7; -.
DR PDBsum; 1MN9; -.
DR PDBsum; 1NCL; -.
DR PDBsum; 1NDC; -.
DR PDBsum; 1NDK; -.
DR PDBsum; 1NDP; -.
DR PDBsum; 1NPK; -.
DR PDBsum; 1NSP; -.
DR PDBsum; 1PAE; -.
DR PDBsum; 1S5Z; -.
DR PDBsum; 2BEF; -.
DR PDBsum; 3FKB; -.
DR PDBsum; 4C6A; -.
DR PDBsum; 4CP5; -.
DR AlphaFoldDB; P22887; -.
DR SMR; P22887; -.
DR STRING; 44689.DDB0185051; -.
DR SWISS-2DPAGE; P22887; -.
DR PaxDb; P22887; -.
DR EnsemblProtists; EAL70593; EAL70593; DDB_G0273805.
DR EnsemblProtists; EAL70752; EAL70752; DDB_G0273069.
DR GeneID; 8618831; -.
DR GeneID; 8619145; -.
DR KEGG; ddi:DDB_G0273069; -.
DR KEGG; ddi:DDB_G0273805; -.
DR dictyBase; DDB_G0273069; ndkC-1.
DR dictyBase; DDB_G0273805; ndkC-2.
DR eggNOG; KOG0888; Eukaryota.
DR HOGENOM; CLU_060216_6_3_1; -.
DR InParanoid; P22887; -.
DR OMA; KIVAMKM; -.
DR PhylomeDB; P22887; -.
DR BRENDA; 2.7.4.6; 1939.
DR EvolutionaryTrace; P22887; -.
DR PRO; PR:P22887; -.
DR Proteomes; UP000002195; Chromosome 2.
DR GO; GO:0005737; C:cytoplasm; IDA:dictyBase.
DR GO; GO:0005856; C:cytoskeleton; IDA:dictyBase.
DR GO; GO:0045335; C:phagocytic vesicle; HDA:dictyBase.
DR GO; GO:0005886; C:plasma membrane; IDA:dictyBase.
DR GO; GO:0005840; C:ribosome; IDA:dictyBase.
DR GO; GO:0030141; C:secretory granule; IDA:dictyBase.
DR GO; GO:0005524; F:ATP binding; IDA:dictyBase.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IDA:dictyBase.
DR GO; GO:0030036; P:actin cytoskeleton organization; IDA:dictyBase.
DR GO; GO:0019954; P:asexual reproduction; IMP:dictyBase.
DR GO; GO:0006241; P:CTP biosynthetic process; IEA:InterPro.
DR GO; GO:0006186; P:dGDP phosphorylation; IDA:dictyBase.
DR GO; GO:0006187; P:dGTP biosynthetic process from dGDP; IDA:dictyBase.
DR GO; GO:0007186; P:G protein-coupled receptor signaling pathway; IMP:dictyBase.
DR GO; GO:0006183; P:GTP biosynthetic process; IEA:InterPro.
DR GO; GO:0045920; P:negative regulation of exocytosis; IMP:dictyBase.
DR GO; GO:0050765; P:negative regulation of phagocytosis; IMP:dictyBase.
DR GO; GO:0048550; P:negative regulation of pinocytosis; IMP:dictyBase.
DR GO; GO:0009142; P:nucleoside triphosphate biosynthetic process; IDA:dictyBase.
DR GO; GO:0009617; P:response to bacterium; HEP:dictyBase.
DR GO; GO:0006414; P:translational elongation; IDA:dictyBase.
DR GO; GO:0006228; P:UTP biosynthetic process; IEA:InterPro.
DR Gene3D; 3.30.70.141; -; 1.
DR HAMAP; MF_00451; NDP_kinase; 1.
DR InterPro; IPR034907; NDK-like_dom.
DR InterPro; IPR036850; NDK-like_dom_sf.
DR InterPro; IPR001564; Nucleoside_diP_kinase.
DR InterPro; IPR023005; Nucleoside_diP_kinase_AS.
DR Pfam; PF00334; NDK; 1.
DR PRINTS; PR01243; NUCDPKINASE.
DR SMART; SM00562; NDK; 1.
DR SUPFAM; SSF54919; SSF54919; 1.
DR PROSITE; PS00469; NDP_KINASES; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Phosphoprotein;
KW Reference proteome; Transferase.
FT CHAIN 1..155
FT /note="Nucleoside diphosphate kinase, cytosolic"
FT /id="PRO_0000137107"
FT ACT_SITE 122
FT /note="Pros-phosphohistidine intermediate"
FT BINDING 16
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 64
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 92
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 98
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 109
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 119
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT HELIX 6..8
FT /evidence="ECO:0007829|PDB:4C6A"
FT STRAND 10..15
FT /evidence="ECO:0007829|PDB:4C6A"
FT HELIX 17..21
FT /evidence="ECO:0007829|PDB:4C6A"
FT HELIX 25..35
FT /evidence="ECO:0007829|PDB:4C6A"
FT STRAND 38..45
FT /evidence="ECO:0007829|PDB:4C6A"
FT HELIX 49..55
FT /evidence="ECO:0007829|PDB:4C6A"
FT HELIX 57..59
FT /evidence="ECO:0007829|PDB:4C6A"
FT STRAND 60..62
FT /evidence="ECO:0007829|PDB:1LWX"
FT HELIX 65..72
FT /evidence="ECO:0007829|PDB:4C6A"
FT STRAND 77..84
FT /evidence="ECO:0007829|PDB:4C6A"
FT HELIX 87..95
FT /evidence="ECO:0007829|PDB:4C6A"
FT HELIX 100..102
FT /evidence="ECO:0007829|PDB:4C6A"
FT HELIX 108..112
FT /evidence="ECO:0007829|PDB:4C6A"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:1LEO"
FT STRAND 121..123
FT /evidence="ECO:0007829|PDB:4C6A"
FT HELIX 127..137
FT /evidence="ECO:0007829|PDB:4C6A"
FT HELIX 140..142
FT /evidence="ECO:0007829|PDB:4C6A"
FT TURN 151..153
FT /evidence="ECO:0007829|PDB:4C6A"
SQ SEQUENCE 155 AA; 16794 MW; 426DB78B1AF2307A CRC64;
MSTNKVNKER TFLAVKPDGV ARGLVGEIIA RYEKKGFVLV GLKQLVPTKD LAESHYAEHK
ERPFFGGLVS FITSGPVVAM VFEGKGVVAS ARLMIGVTNP LASAPGSIRG DFGVDVGRNI
IHGSDSVESA NREIALWFKP EELLTEVKPN PNLYE
