NDK_HELPG
ID NDK_HELPG Reviewed; 137 AA.
AC B5Z9W9;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 25-NOV-2008, sequence version 1.
DT 03-AUG-2022, entry version 73.
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=HPG27_182;
OS Helicobacter pylori (strain G27).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Campylobacterales;
OC Helicobacteraceae; Helicobacter.
OX NCBI_TaxID=563041;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=G27;
RX PubMed=18952803; DOI=10.1128/jb.01416-08;
RA Baltrus D.A., Amieva M.R., Covacci A., Lowe T.M., Merrell D.S.,
RA Ottemann K.M., Stein M., Salama N.R., Guillemin K.;
RT "The complete genome sequence of Helicobacter pylori strain G27.";
RL J. Bacteriol. 191:447-448(2009).
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; CP001173; ACI26949.1; -; Genomic_DNA.
DR RefSeq; WP_000813730.1; NC_011333.1.
DR PDB; 6AY1; X-ray; 2.05 A; A/B/C/D/E/F/G/H=1-137.
DR PDBsum; 6AY1; -.
DR AlphaFoldDB; B5Z9W9; -.
DR SMR; B5Z9W9; -.
DR EnsemblBacteria; ACI26949; ACI26949; HPG27_182.
DR KEGG; hpg:HPG27_182; -.
DR HOGENOM; CLU_060216_8_1_7; -.
DR OMA; KIVAMKM; -.
DR OrthoDB; 1752581at2; -.
DR BRENDA; 2.7.4.6; 2604.
DR Proteomes; UP000001735; 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..137
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_1000192260"
FT ACT_SITE 116
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 10
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 58
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 86
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 92
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 103
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 113
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT STRAND 2..9
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 11..15
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 19..27
FT /evidence="ECO:0007829|PDB:6AY1"
FT TURN 28..30
FT /evidence="ECO:0007829|PDB:6AY1"
FT STRAND 32..39
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 43..49
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 59..67
FT /evidence="ECO:0007829|PDB:6AY1"
FT STRAND 71..79
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 81..89
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 94..96
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 102..106
FT /evidence="ECO:0007829|PDB:6AY1"
FT STRAND 114..117
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 121..131
FT /evidence="ECO:0007829|PDB:6AY1"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:6AY1"
SQ SEQUENCE 137 AA; 15300 MW; 2089FD0570E5BC70 CRC64;
MKQRTLSIIK PDALKKKVVG KIIDRFESNG LEVIAMKRLH LSVKDAENFY AIHRERPFFK
DLIEFMVSGP VVVMVLEGKD AVAKNRDLMG ATDPKLAQKG TIRADFAESI DANAVHGSDS
LENAHNEIAF FFAARDL
