NDK_STAAC
ID NDK_STAAC Reviewed; 149 AA.
AC Q5HFV4;
DT 07-JUN-2005, integrated into UniProtKB/Swiss-Prot.
DT 15-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 100.
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=SACOL1509;
OS Staphylococcus aureus (strain COL).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93062;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=COL;
RX PubMed=15774886; DOI=10.1128/jb.187.7.2426-2438.2005;
RA Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J.,
RA Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J.,
RA Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H.,
RA Vamathevan J.J., Khouri H., Utterback T.R., Lee C., Dimitrov G., Jiang L.,
RA Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E.,
RA Fraser C.M.;
RT "Insights on evolution of virulence and resistance from the complete genome
RT analysis of an early methicillin-resistant Staphylococcus aureus strain and
RT a biofilm-producing methicillin-resistant Staphylococcus epidermidis
RT strain.";
RL J. Bacteriol. 187:2426-2438(2005).
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; CP000046; AAW36704.1; -; Genomic_DNA.
DR RefSeq; WP_000442480.1; NC_002951.2.
DR PDB; 3Q83; X-ray; 2.50 A; A/B/C/D/E/F=1-149.
DR PDB; 3Q86; X-ray; 2.38 A; A/B=1-149.
DR PDB; 3Q89; X-ray; 2.90 A; A/B/C/D/E/F/G/H=1-149.
DR PDB; 3Q8U; X-ray; 2.22 A; A/B/C/D/E/F=1-149.
DR PDB; 3Q8V; X-ray; 2.50 A; A/B/C/D/E/F/G/H=1-149.
DR PDB; 3Q8Y; X-ray; 2.70 A; A/B/C/D/E/F/G/H=1-149.
DR PDBsum; 3Q83; -.
DR PDBsum; 3Q86; -.
DR PDBsum; 3Q89; -.
DR PDBsum; 3Q8U; -.
DR PDBsum; 3Q8V; -.
DR PDBsum; 3Q8Y; -.
DR AlphaFoldDB; Q5HFV4; -.
DR SMR; Q5HFV4; -.
DR EnsemblBacteria; AAW36704; AAW36704; SACOL1509.
DR GeneID; 66839658; -.
DR KEGG; sac:SACOL1509; -.
DR HOGENOM; CLU_060216_6_3_9; -.
DR OMA; KIVAMKM; -.
DR EvolutionaryTrace; Q5HFV4; -.
DR Proteomes; UP000000530; 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..149
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000137044"
FT ACT_SITE 115
FT /note="Pros-phosphohistidine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 9
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 85
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 91
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 102
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT BINDING 112
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00451"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 10..14
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 18..27
FT /evidence="ECO:0007829|PDB:3Q8U"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 42..48
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 58..65
FT /evidence="ECO:0007829|PDB:3Q8U"
FT STRAND 70..77
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 80..88
FT /evidence="ECO:0007829|PDB:3Q8U"
FT TURN 93..95
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 101..105
FT /evidence="ECO:0007829|PDB:3Q8U"
FT STRAND 108..111
FT /evidence="ECO:0007829|PDB:3Q8Y"
FT STRAND 113..116
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 120..130
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 133..135
FT /evidence="ECO:0007829|PDB:3Q8U"
FT HELIX 144..147
FT /evidence="ECO:0007829|PDB:3Q8U"
SQ SEQUENCE 149 AA; 16575 MW; D7E3E0444443226E CRC64;
MERTFLMIKP DAVQRNLIGE VISRIERKGL KLVGGKLMQV PMELAETHYG EHQGKPFYND
LISFITSAPV FAMVVEGEDA VNVSRHIIGS TNPSEASPGS IRGDLGLTVG RNIIHGSDSL
ESAEREINLW FNENEITSYA SPRDAWLYE
