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 27-MAR-2024, entry version 183. 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 (Social amoeba). 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}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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.P22887; -. DR PaxDb; 44689-DDB0185051; -. 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; QHYGEHK; -. DR PhylomeDB; P22887; -. DR BRENDA; 2.7.4.6; 1939. DR Reactome; R-DDI-499943; Interconversion of nucleotide di- and triphosphates. DR Reactome; R-DDI-6798695; Neutrophil degranulation. DR Reactome; R-DDI-9748787; Azathioprine ADME. DR Reactome; R-DDI-9755088; Ribavirin ADME. 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: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:0016310; P:phosphorylation; IEA:UniProtKB-KW. 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 CDD; cd04413; NDPk_I; 1. DR Gene3D; 3.30.70.141; Nucleoside diphosphate kinase-like domain; 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 PANTHER; PTHR11349; NUCLEOSIDE DIPHOSPHATE KINASE; 1. DR PANTHER; PTHR11349:SF91; NUCLEOSIDE DIPHOSPHATE KINASE; 1. DR Pfam; PF00334; NDK; 1. DR PRINTS; PR01243; NUCDPKINASE. DR SMART; SM00562; NDK; 1. DR SUPFAM; SSF54919; Nucleoside diphosphate kinase, NDK; 1. DR PROSITE; PS00469; NDPK; 1. DR PROSITE; PS51374; NDPK_LIKE; 1. DR SWISS-2DPAGE; P22887; -. 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 //