ID D1BZN5_XYLCX Unreviewed; 151 AA.
AC D1BZN5;
DT 19-JAN-2010, integrated into UniProtKB/TrEMBL.
DT 19-JAN-2010, sequence version 1.
DT 27-MAR-2024, entry version 72.
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 OrderedLocusNames=Xcel_1158 {ECO:0000313|EMBL:ACZ30189.1};
OS Xylanimonas cellulosilytica (strain DSM 15894 / CECT 5975 / LMG 20990 /
OS XIL07).
OC Bacteria; Actinomycetota; Actinomycetes; Micrococcales;
OC Promicromonosporaceae; Xylanimonas.
OX NCBI_TaxID=446471 {ECO:0000313|EMBL:ACZ30189.1, ECO:0000313|Proteomes:UP000002255};
RN [1] {ECO:0000313|Proteomes:UP000002255}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 15894 / CECT 5975 / LMG 20990 / XIL07
RC {ECO:0000313|Proteomes:UP000002255};
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Kyrpides N., Mavromatis K., Ivanova N.,
RA Mikhailova N., Foster B., Clum A., Brettin T., Detter J.C., Han C.,
RA Larimer F., Land M., Hauser L., Markowitz V., Cheng J.F., Hugenholtz P.,
RA Woyke T., Wu D., Gehrich-Schroeter G., Schneider S., Pukall S.R.,
RA Klenk H.P., Eisen J.A.;
RT "The complete chromosome of Xylanimonas cellulosilytica DSM 15894.";
RL Submitted (NOV-2009) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ACZ30189.1, ECO:0000313|Proteomes:UP000002255}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 15894 / CECT 5975 / LMG 20990 / XIL07
RC {ECO:0000313|Proteomes:UP000002255};
RX PubMed=21304672; DOI=10.4056/sigs.571102;
RA Foster B., Pukall R., Abt B., Nolan M., Glavina Del Rio T., Chen F.,
RA Lucas S., Tice H., Pitluck S., Cheng J.-F., Chertkov O., Brettin T.,
RA Han C., Detter J.C., Bruce D., Goodwin L., Ivanova N., Mavromatis K.,
RA Pati A., Mikhailova N., Chen A., Palaniappan K., Land M., Hauser L.,
RA Chang Y.-J., Jeffries C.D., Chain P., Rohde M., Goeker M., Bristow J.,
RA Eisen J.A., Markowitz V., Hugenholtz P., Kyrpides N.C., Klenk H.-P.,
RA Lapidus A.;
RT "Complete genome sequence of Xylanimonas cellulosilytica type strain
RT (XIL07).";
RL Stand. Genomic Sci. 2:1-8(2010).
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|ARBA:ARBA00001946,
CC 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; CP001821; ACZ30189.1; -; Genomic_DNA.
DR RefSeq; WP_012877931.1; NC_013530.1.
DR AlphaFoldDB; D1BZN5; -.
DR STRING; 446471.Xcel_1158; -.
DR KEGG; xce:Xcel_1158; -.
DR eggNOG; COG0105; Bacteria.
DR HOGENOM; CLU_060216_6_3_11; -.
DR OrthoDB; 9801161at2; -.
DR Proteomes; UP000002255; 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 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; NDP_KINASES; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_00451}; Cytoplasm {ECO:0000256|HAMAP-Rule:MF_00451};
KW Kinase {ECO:0000256|HAMAP-Rule:MF_00451, ECO:0000256|RuleBase:RU004013};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00451};
KW Metal-binding {ECO:0000256|HAMAP-Rule:MF_00451};
KW Nucleotide metabolism {ECO:0000256|HAMAP-Rule:MF_00451};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_00451}; Phosphoprotein {ECO:0000256|HAMAP-Rule:MF_00451};
KW Reference proteome {ECO:0000313|Proteomes:UP000002255};
KW Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW Rule:MF_00451}.
FT DOMAIN 14..151
FT /note="Nucleoside diphosphate kinase-like"
FT /evidence="ECO:0000259|SMART:SM00562"
FT ACT_SITE 132
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 22
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 70
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 98
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 115
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT BINDING 129
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
SQ SEQUENCE 151 AA; 16319 MW; 26F14CF20C77FEAF CRC64;
MTTQTPPETN DPTVERTLVL VKPDGVRRGL SGEVLRRVEA KGYTLVAVEL LDATPGLLAE
HYAEHVGKEF YQPLVDFMMS GPILAVAIEG QRVVEGFRSL AGATDGTLAS PGTIRGDFAR
SWGSKVMQNI VHGSDSPESA AREIALWFPK L
//
