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Database: UniProt
Entry: A0A062V972_9EURY
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ID   A0A062V972_9EURY        Unreviewed;       147 AA.
AC   A0A062V972;
DT   03-SEP-2014, integrated into UniProtKB/TrEMBL.
DT   03-SEP-2014, sequence version 1.
DT   24-JAN-2024, entry version 31.
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=ANME2D_01951 {ECO:0000313|EMBL:KCZ71895.1};
OS   Candidatus Methanoperedens nitroreducens.
OC   Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC   Methanosarcinales; Candidatus Methanoperedenaceae;
OC   Candidatus Methanoperedens.
OX   NCBI_TaxID=1392998 {ECO:0000313|EMBL:KCZ71895.1, ECO:0000313|Proteomes:UP000027153};
RN   [1] {ECO:0000313|EMBL:KCZ71895.1, ECO:0000313|Proteomes:UP000027153}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ANME-2d {ECO:0000313|EMBL:KCZ71895.1,
RC   ECO:0000313|Proteomes:UP000027153};
RX   PubMed=23892779; DOI=10.1038/nature12375;
RA   Haroon M.F., Hu S., Shi Y., Imelfort M., Keller J., Hugenholtz P., Yuan Z.,
RA   Tyson G.W.;
RT   "Anaerobic oxidation of methane coupled to nitrate reduction in a novel
RT   archaeal lineage.";
RL   Nature 500:567-570(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|ARBA:ARBA00001946,
CC         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:KCZ71895.1}.
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DR   EMBL; JMIY01000004; KCZ71895.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A062V972; -.
DR   PATRIC; fig|1392998.3.peg.1950; -.
DR   Proteomes; UP000027153; 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; 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:UP000027153};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679, ECO:0000256|HAMAP-
KW   Rule:MF_00451}.
FT   DOMAIN          1..132
FT                   /note="Nucleoside diphosphate kinase-like"
FT                   /evidence="ECO:0000259|SMART:SM00562"
FT   ACT_SITE        109
FT                   /note="Pros-phosphohistidine intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT   BINDING         3
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT   BINDING         51
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT   BINDING         79
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         96
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
FT   BINDING         106
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00451"
SQ   SEQUENCE   147 AA;  16286 MW;  A415400D70844416 CRC64;
     MVKPDGVQRG LVGEVMSRIE RRGLKIVALR MSTISRELAK EHYAEHVEKP FFNSLVDFIT
     SGPSVSMVVE GKNAVSVMRA INGATNPANA ATGSIRGDFA LDTGRNIVHA SDSPESARRE
     IDIHFEESEI IQYSRVDENW LYEQANP
//
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