NDK_ECOLI
ID NDK_ECOLI Reviewed; 143 AA.
AC P0A763; P24233;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 2.
DT 03-AUG-2022, entry version 140.
DE RecName: Full=Nucleoside diphosphate kinase {ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000303|PubMed:1657712};
DE Short=NDK {ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000303|PubMed:1657712};
DE Short=NDP kinase {ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000303|PubMed:1657712};
DE EC=2.7.4.6 {ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000269|PubMed:7730286};
DE AltName: Full=Nucleoside-2-P kinase {ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000305};
GN Name=ndk {ECO:0000255|HAMAP-Rule:MF_00451, ECO:0000303|PubMed:1657712};
GN OrderedLocusNames=b2518, JW2502;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=K12;
RX PubMed=1657712; DOI=10.1016/0378-1119(91)90510-i;
RA Hama H., Almaula N., Lerner C.G., Inouye S., Inouye M.;
RT "Nucleoside diphosphate kinase from Escherichia coli; its overproduction
RT and sequence comparison with eukaryotic enzymes.";
RL Gene 105:31-36(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=9205837; DOI=10.1093/dnares/4.2.91;
RA Yamamoto Y., Aiba H., Baba T., Hayashi K., Inada T., Isono K., Itoh T.,
RA Kimura S., Kitagawa M., Makino K., Miki T., Mitsuhashi N., Mizobuchi K.,
RA Mori H., Nakade S., Nakamura Y., Nashimoto H., Oshima T., Oyama S.,
RA Saito N., Sampei G., Satoh Y., Sivasundaram S., Tagami H., Takahashi H.,
RA Takeda J., Takemoto K., Uehara K., Wada C., Yamagata S., Horiuchi T.;
RT "Construction of a contiguous 874-kb sequence of the Escherichia coli-K12
RT genome corresponding to 50.0-68.8 min on the linkage map and analysis of
RT its sequence features.";
RL DNA Res. 4:91-113(1997).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP PROTEIN SEQUENCE OF 2-46.
RX PubMed=1323446; DOI=10.1016/b978-0-12-152833-1.50025-3;
RA Ray N.B., Mathews C.K.;
RT "Nucleoside diphosphokinase: a functional link between intermediary
RT metabolism and nucleic acid synthesis.";
RL Curr. Top. Cell. Regul. 33:343-357(1992).
RN [6]
RP PROTEIN SEQUENCE OF 2-12.
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RA Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F.;
RL Submitted (FEB-1996) to UniProtKB.
RN [7]
RP PARTIAL PROTEIN SEQUENCE, FUNCTION, CATALYTIC ACTIVITY, SUBUNIT,
RP PHOSPHORYLATION AT SER-119 AND SER-121, AND MUTAGENESIS OF SER-119 AND
RP SER-121.
RX PubMed=7730286; DOI=10.1128/jb.177.9.2524-2529.1995;
RA Almaula N., Lu Q., Delgado J., Belkin S., Inouye M.;
RT "Nucleoside diphosphate kinase from Escherichia coli.";
RL J. Bacteriol. 177:2524-2529(1995).
RN [8] {ECO:0007744|PDB:2HUR}
RP X-RAY CRYSTALLOGRAPHY (1.62 ANGSTROMS) OF 2-143, AND SUBUNIT.
RX PubMed=17330300; DOI=10.1002/prot.21316;
RA Moynie L., Giraud M.F., Georgescauld F., Lascu I., Dautant A.;
RT "The structure of the Escherichia coli nucleoside diphosphate kinase
RT reveals a new quaternary architecture for this enzyme family.";
RL Proteins 67:755-765(2007).
CC -!- FUNCTION: Major role in the synthesis of nucleoside triphosphates other
CC than ATP. The ATP gamma phosphate is transferred to the NDP beta
CC phosphate via a ping-pong mechanism, using a phosphorylated active-site
CC intermediate. {ECO:0000255|HAMAP-Rule:MF_00451,
CC ECO:0000269|PubMed:7730286}.
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; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00451, ECO:0000269|PubMed:7730286};
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 Evidence={ECO:0000255|HAMAP-Rule:MF_00451,
CC ECO:0000269|PubMed:7730286};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00451};
CC -!- SUBUNIT: Homotetramer. {ECO:0000255|HAMAP-Rule:MF_00451,
CC ECO:0000269|PubMed:17330300, ECO:0000269|PubMed:7730286}.
CC -!- INTERACTION:
CC P0A763; P12295: ung; NbExp=3; IntAct=EBI-370139, EBI-559403;
CC P0A763; P0AC28: ygfA; NbExp=5; IntAct=EBI-370139, EBI-555094;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00451,
CC ECO:0000305}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000255|HAMAP-
CC Rule:MF_00451, ECO:0000305}.
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DR EMBL; X57555; CAA40780.1; -; Genomic_DNA.
DR EMBL; U00096; AAC75571.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA16405.1; -; Genomic_DNA.
DR PIR; JH0495; JH0495.
DR RefSeq; NP_417013.1; NC_000913.3.
DR RefSeq; WP_000963837.1; NZ_STEB01000011.1.
DR PDB; 2HUR; X-ray; 1.62 A; A/B/C/D/E/F=2-143.
DR PDBsum; 2HUR; -.
DR AlphaFoldDB; P0A763; -.
DR SMR; P0A763; -.
DR BioGRID; 4259709; 42.
DR BioGRID; 849983; 1.
DR DIP; DIP-31870N; -.
DR IntAct; P0A763; 7.
DR STRING; 511145.b2518; -.
DR iPTMnet; P0A763; -.
DR SWISS-2DPAGE; P0A763; -.
DR jPOST; P0A763; -.
DR PaxDb; P0A763; -.
DR PRIDE; P0A763; -.
DR EnsemblBacteria; AAC75571; AAC75571; b2518.
DR EnsemblBacteria; BAA16405; BAA16405; BAA16405.
DR GeneID; 67416902; -.
DR GeneID; 945611; -.
DR KEGG; ecj:JW2502; -.
DR KEGG; eco:b2518; -.
DR PATRIC; fig|1411691.4.peg.4218; -.
DR EchoBASE; EB0644; -.
DR eggNOG; COG0105; Bacteria.
DR HOGENOM; CLU_060216_8_1_6; -.
DR InParanoid; P0A763; -.
DR OMA; KIVAMKM; -.
DR PhylomeDB; P0A763; -.
DR BioCyc; EcoCyc:NUCLEOSIDE-DIP-KIN-MON; -.
DR BioCyc; MetaCyc:NUCLEOSIDE-DIP-KIN-MON; -.
DR BRENDA; 2.7.4.6; 2026.
DR EvolutionaryTrace; P0A763; -.
DR PRO; PR:P0A763; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IDA:EcoCyc.
DR GO; GO:0006241; P:CTP biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006183; P:GTP biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IEA:InterPro.
DR GO; GO:0006163; P:purine nucleotide metabolic process; IBA:GO_Central.
DR GO; GO:0006220; P:pyrimidine nucleotide metabolic process; IBA:GO_Central.
DR GO; GO:0006228; P:UTP biosynthetic process; IEA:UniProtKB-UniRule.
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; Direct protein sequencing; Kinase;
KW Magnesium; Metal-binding; Nucleotide metabolism; Nucleotide-binding;
KW Phosphoprotein; Reference proteome; Transferase.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:1323446, ECO:0000269|Ref.6"
FT CHAIN 2..143
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000136978"
FT ACT_SITE 117
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P15531, ECO:0000255|HAMAP-
FT Rule:MF_00451"
FT BINDING 11
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 59
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 87
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 93
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 104
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 114
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT MOD_RES 119
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:7730286"
FT MOD_RES 121
FT /note="Phosphoserine"
FT /evidence="ECO:0000269|PubMed:7730286"
FT MUTAGEN 119
FT /note="S->A: Still autophosphorylates. No change in kinase
FT activity."
FT /evidence="ECO:0000269|PubMed:7730286"
FT MUTAGEN 121
FT /note="S->A: Still autophosphorylates. No change in kinase
FT activity."
FT /evidence="ECO:0000269|PubMed:7730286"
FT STRAND 3..10
FT /evidence="ECO:0007829|PDB:2HUR"
FT HELIX 12..16
FT /evidence="ECO:0007829|PDB:2HUR"
FT HELIX 20..29
FT /evidence="ECO:0007829|PDB:2HUR"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:2HUR"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:2HUR"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:2HUR"
FT HELIX 60..67
FT /evidence="ECO:0007829|PDB:2HUR"
FT STRAND 72..80
FT /evidence="ECO:0007829|PDB:2HUR"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:2HUR"
FT TURN 95..97
FT /evidence="ECO:0007829|PDB:2HUR"
FT HELIX 103..107
FT /evidence="ECO:0007829|PDB:2HUR"
FT STRAND 109..111
FT /evidence="ECO:0007829|PDB:2HUR"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:2HUR"
FT HELIX 122..132
FT /evidence="ECO:0007829|PDB:2HUR"
SQ SEQUENCE 143 AA; 15463 MW; 8C069C10043532EC CRC64;
MAIERTFSII KPNAVAKNVI GNIFARFEAA GFKIVGTKML HLTVEQARGF YAEHDGKPFF
DGLVEFMTSG PIVVSVLEGE NAVQRHRDLL GATNPANALA GTLRADYADS LTENGTHGSD
SVESAAREIA YFFGEGEVCP RTR
