ID A0A0D2I0X5_9BACT Unreviewed; 135 AA.
AC A0A0D2I0X5;
DT 29-APR-2015, integrated into UniProtKB/TrEMBL.
DT 29-APR-2015, sequence version 1.
DT 27-MAR-2024, entry version 28.
DE RecName: Full=Nucleoside diphosphate kinase {ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000256|RuleBase:RU004013};
DE Short=NDK {ECO:0000256|HAMAP-Rule:MF_00451};
DE Short=NDP kinase {ECO:0000256|HAMAP-Rule:MF_00451};
DE EC=2.7.4.6 {ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000256|RuleBase:RU004013};
DE AltName: Full=Nucleoside-2-P kinase {ECO:0000256|HAMAP-Rule:MF_00451};
GN Name=ndk {ECO:0000256|HAMAP-Rule:MF_00451};
GN ORFNames=J120_05135 {ECO:0000313|EMBL:KIX84880.1};
OS candidate division TM6 bacterium JCVI TM6SC1.
OC Bacteria; Candidatus Dependentiae; Vermiphilus.
OX NCBI_TaxID=1306947 {ECO:0000313|EMBL:KIX84880.1, ECO:0000313|Proteomes:UP000032214};
RN [1] {ECO:0000313|EMBL:KIX84880.1, ECO:0000313|Proteomes:UP000032214}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=TM6SC1 {ECO:0000313|EMBL:KIX84880.1,
RC ECO:0000313|Proteomes:UP000032214};
RX PubMed=23754396; DOI=10.1073/pnas.1219809110;
RA McLean J.S., Lombardo M.J., Badger J.H., Edlund A., Novotny M.,
RA Yee-Greenbaum J., Vyahhi N., Hall A.P., Yang Y., Dupont C.L., Ziegler M.G.,
RA Chitsaz H., Allen A.E., Yooseph S., Tesler G., Pevzner P.A., Friedman R.M.,
RA Nealson K.H., Venter J.C., Lasken R.S.;
RT "Candidate phylum TM6 genome recovered from a hospital sink biofilm
RT provides genomic insights into this uncultivated phylum.";
RL Proc. Natl. Acad. Sci. U.S.A. 110:E2390-E2399(2013).
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:0000256|HAMAP-Rule:MF_00451}.
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:0000256|HAMAP-
CC Rule:MF_00451, ECO:0000256|RuleBase:RU004013};
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:0000256|HAMAP-Rule:MF_00451};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_00451};
CC -!- SUBUNIT: Homotetramer. {ECO:0000256|HAMAP-Rule:MF_00451}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00451}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000256|ARBA:ARBA00008142,
CC ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000256|RuleBase:RU004011}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KIX84880.1}.
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DR EMBL; ARQD01000007; KIX84880.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A0D2I0X5; -.
DR STRING; 1306947.J120_05135; -.
DR eggNOG; COG0105; Bacteria.
DR Proteomes; UP000032214; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
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; IEA:UniProtKB-UniRule.
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:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0006228; P:UTP biosynthetic process; IEA:UniProtKB-UniRule.
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; PTHR46161; NUCLEOSIDE DIPHOSPHATE KINASE; 1.
DR PANTHER; PTHR46161:SF3; NUCLEOSIDE DIPHOSPHATE KINASE DDB_G0292928-RELATED; 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; NDP_KINASES; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_00451};
KW Cytoplasm {ECO:0000256|ARBA:ARBA00022490, ECO:0000256|HAMAP-Rule:MF_00451};
KW Kinase {ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000256|RuleBase:RU004013};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00451};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_00451}; Nucleotide metabolism {ECO:0000256|HAMAP-Rule:MF_00451};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00451,
KW ECO:0000256|RuleBase:RU004013};
KW Phosphoprotein {ECO:0000256|HAMAP-Rule:MF_00451};
KW Reference proteome {ECO:0000313|Proteomes:UP000032214};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00451}.
FT DOMAIN 1..134
FT /note="Nucleoside diphosphate kinase-like"
FT /evidence="ECO:0000259|SMART:SM00562"
FT ACT_SITE 115
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 9
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 85
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 102
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 112
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
SQ SEQUENCE 135 AA; 14937 MW; 0F4C1C1A457B5AA2 CRC64;
MQNTFAMIKP DAVSKKYSGK IIDMVEQNGF DIVRMHKVRL TKEGAHQLYA IHKDRPFFNE
MVDFITSGPL IIMVLAKDNA IQAWRDLLGA TDPSKAAPGT IRSMFGSSIG NNAAHGSDSP
ENAAQELKLF FPDLK
//
