ID I1XLT8_METNJ Unreviewed; 143 AA.
AC I1XLT8;
DT 11-JUL-2012, integrated into UniProtKB/TrEMBL.
DT 11-JUL-2012, sequence version 1.
DT 27-MAR-2024, entry version 54.
DE RecName: Full=Nucleoside diphosphate kinase {ECO:0000256|HAMAP-Rule:MF_00451};
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};
DE AltName: Full=Nucleoside-2-P kinase {ECO:0000256|HAMAP-Rule:MF_00451};
GN Name=ndk {ECO:0000256|HAMAP-Rule:MF_00451};
GN OrderedLocusNames=Q7A_2564 {ECO:0000313|EMBL:AFI85357.1};
GN ORFNames=CDW43_11310 {ECO:0000313|EMBL:AUZ85121.1};
OS Methylophaga nitratireducenticrescens.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Thiotrichales;
OC Piscirickettsiaceae; Methylophaga.
OX NCBI_TaxID=754476 {ECO:0000313|EMBL:AFI85357.1, ECO:0000313|Proteomes:UP000009144};
RN [1] {ECO:0000313|EMBL:AFI85357.1, ECO:0000313|Proteomes:UP000009144}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=JAM1 {ECO:0000313|EMBL:AFI85357.1,
RC ECO:0000313|Proteomes:UP000009144};
RX PubMed=22815445; DOI=10.1128/JB.00726-12;
RA Villeneuve C., Martineau C., Mauffrey F., Villemur R.;
RT "Complete genome sequences of Methylophaga sp. strain JAM1 and Methylophaga
RT sp. strain JAM7.";
RL J. Bacteriol. 194:4126-4127(2012).
RN [2] {ECO:0000313|EMBL:AFI85357.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=JAM1 {ECO:0000313|EMBL:AFI85357.1};
RX PubMed=23148104; DOI=10.1099/ijs.0.044545-0;
RA Villeneuve C., Martineau C., Mauffrey F., Villemur R.;
RT "Methylophaga nitratireducenticrescens sp. nov. and Methylophaga frappieri
RT sp. nov., isolated from the biofilm of the methanol-fed denitrification
RT system treating the seawater at the Montreal Biodome.";
RL Int. J. Syst. Evol. Microbiol. 63:2216-2222(2013).
RN [3] {ECO:0000313|EMBL:AFI85357.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=JAM1 {ECO:0000313|EMBL:AFI85357.1};
RA Villeneuve C., Villemur R.;
RL Submitted (JUN-2015) to the EMBL/GenBank/DDBJ databases.
RN [4] {ECO:0000313|EMBL:AUZ85121.1, ECO:0000313|Proteomes:UP000238402}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GP59 {ECO:0000313|EMBL:AUZ85121.1,
RC ECO:0000313|Proteomes:UP000238402};
RA Villemur R.;
RT "The sequence of the genome of Methylophaga nitratireducenticrescens GP59
RT and its two plasmids.";
RL Submitted (JUN-2017) to the EMBL/GenBank/DDBJ databases.
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};
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}.
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DR EMBL; CP003390; AFI85357.1; -; Genomic_DNA.
DR EMBL; CP021973; AUZ85121.1; -; Genomic_DNA.
DR RefSeq; WP_014707719.1; NZ_CP021973.1.
DR AlphaFoldDB; I1XLT8; -.
DR STRING; 754476.Q7A_2564; -.
DR KEGG; mej:Q7A_2564; -.
DR PATRIC; fig|754476.3.peg.2518; -.
DR eggNOG; COG0105; Bacteria.
DR HOGENOM; CLU_060216_8_1_6; -.
DR OrthoDB; 9801161at2; -.
DR Proteomes; UP000009144; Chromosome.
DR Proteomes; UP000238402; Chromosome.
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 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.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|HAMAP-Rule:MF_00451};
KW Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00451};
KW Kinase {ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000313|EMBL:AFI85357.1};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00451};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00451};
KW Nucleotide metabolism {ECO:0000256|ARBA:ARBA00023080, ECO:0000256|HAMAP-
KW Rule:MF_00451}; Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00451};
KW Phosphoprotein {ECO:0000256|HAMAP-Rule:MF_00451};
KW Transferase {ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000313|EMBL:AFI85357.1}.
FT DOMAIN 3..140
FT /note="Nucleoside diphosphate kinase-like"
FT /evidence="ECO:0000259|SMART:SM00562"
FT ACT_SITE 117
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 11
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 59
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 87
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 93
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 104
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 114
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
SQ SEQUENCE 143 AA; 15521 MW; 5D5A0E2C6039189B CRC64;
MATERTLSII KPDAVAKNVI GEIYSRFEKA GLSIVAARMV HLSQQQAEGF YAEHKARPFF
GDLVSFMTSG PVMIQVLEGE NAVVTHRDLM GATNPADAAP GTIRADFAQS IDENAVHGSD
SAESAAREIA YFFTEDQLCA RTR
//
