NDK_NEIG2
ID NDK_NEIG2 Reviewed; 141 AA.
AC B4RMG0;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 23-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 68.
DE RecName: Full=Nucleoside diphosphate kinase {ECO:0000255|HAMAP-Rule:MF_00451};
DE Short=NDK {ECO:0000255|HAMAP-Rule:MF_00451};
DE Short=NDP kinase {ECO:0000255|HAMAP-Rule:MF_00451};
DE EC=2.7.4.6 {ECO:0000255|HAMAP-Rule:MF_00451};
DE AltName: Full=Nucleoside-2-P kinase {ECO:0000255|HAMAP-Rule:MF_00451};
GN Name=ndk {ECO:0000255|HAMAP-Rule:MF_00451}; OrderedLocusNames=NGK_1320;
OS Neisseria gonorrhoeae (strain NCCP11945).
OC Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC Neisseria.
OX NCBI_TaxID=521006;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCCP11945;
RX PubMed=18586945; DOI=10.1128/jb.00566-08;
RA Chung G.T., Yoo J.S., Oh H.B., Lee Y.S., Cha S.H., Kim S.J., Yoo C.K.;
RT "Complete genome sequence of Neisseria gonorrhoeae NCCP11945.";
RL J. Bacteriol. 190:6035-6036(2008).
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 -!- 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};
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 -!- 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 -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00451}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000255|HAMAP-
CC Rule:MF_00451}.
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DR EMBL; CP001050; ACF29995.1; -; Genomic_DNA.
DR RefSeq; WP_003688947.1; NC_011035.1.
DR PDB; 5V6D; X-ray; 1.85 A; A/B/C/D/E/F/G/H/I/J/K/L/M/N/O/P=1-141.
DR PDBsum; 5V6D; -.
DR AlphaFoldDB; B4RMG0; -.
DR SMR; B4RMG0; -.
DR EnsemblBacteria; ACF29995; ACF29995; NGK_1320.
DR GeneID; 66752936; -.
DR KEGG; ngk:NGK_1320; -.
DR HOGENOM; CLU_060216_8_1_4; -.
DR OMA; KIVAMKM; -.
DR OrthoDB; 1752581at2; -.
DR BRENDA; 2.7.4.6; 3590.
DR Proteomes; UP000002564; 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:0006165; P:nucleoside diphosphate phosphorylation; IEA:InterPro.
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; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Phosphoprotein; Transferase.
FT CHAIN 1..141
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_1000192278"
FT ACT_SITE 117
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000255|HAMAP-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 STRAND 3..10
FT /evidence="ECO:0007829|PDB:5V6D"
FT HELIX 12..16
FT /evidence="ECO:0007829|PDB:5V6D"
FT HELIX 20..28
FT /evidence="ECO:0007829|PDB:5V6D"
FT TURN 29..31
FT /evidence="ECO:0007829|PDB:5V6D"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:5V6D"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:5V6D"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:5V6D"
FT HELIX 60..68
FT /evidence="ECO:0007829|PDB:5V6D"
FT STRAND 72..80
FT /evidence="ECO:0007829|PDB:5V6D"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:5V6D"
FT TURN 95..97
FT /evidence="ECO:0007829|PDB:5V6D"
FT HELIX 103..107
FT /evidence="ECO:0007829|PDB:5V6D"
FT STRAND 110..113
FT /evidence="ECO:0007829|PDB:5V6D"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:5V6D"
FT HELIX 122..132
FT /evidence="ECO:0007829|PDB:5V6D"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:5V6D"
SQ SEQUENCE 141 AA; 15441 MW; 90E8C01ED540878C CRC64;
MAIERTISII KPDAVGKNVI GKIYSRFEEN GLKIVAAKMK QLTLKEAQEF YAVHKDRPFY
AGLVEFMTGG PVMIQVLEGE NAVLKNRELM GATNPTEAAE GTIRADFATS VSINAVHGSD
SVENAALEIA YFFSQTEICP R
