NDK_ACIBS
ID NDK_ACIBS Reviewed; 143 AA.
AC B0VKS3;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 10-JUN-2008, sequence version 1.
DT 03-AUG-2022, entry version 84.
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=ABSDF3006;
OS Acinetobacter baumannii (strain SDF).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Moraxellales; Moraxellaceae;
OC Acinetobacter; Acinetobacter calcoaceticus/baumannii complex.
OX NCBI_TaxID=509170;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SDF;
RX PubMed=18350144; DOI=10.1371/journal.pone.0001805;
RA Vallenet D., Nordmann P., Barbe V., Poirel L., Mangenot S., Bataille E.,
RA Dossat C., Gas S., Kreimeyer A., Lenoble P., Oztas S., Poulain J.,
RA Segurens B., Robert C., Abergel C., Claverie J.-M., Raoult D., Medigue C.,
RA Weissenbach J., Cruveiller S.;
RT "Comparative analysis of Acinetobacters: three genomes for three
RT lifestyles.";
RL PLoS ONE 3:E1805-E1805(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 -!- FUNCTION: (Microbial infection) Catalyzes the phosphorylation of dZDP
CC to dZTP, when the bacterium is infected by a phage that produces the
CC substrate for the synthesis of dZTP (2- amino-2'-deoxyadenosine 5'-
CC triphosphate), which is then used by the phage as a DNA polymerase
CC substrate. {ECO:0000250|UniProtKB:Q9KNM4}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + dZDP = ADP + dZTP; Xref=Rhea:RHEA:67644,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:172929, ChEBI:CHEBI:172931,
CC ChEBI:CHEBI:456216; Evidence={ECO:0000250|UniProtKB:Q9KTX4};
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 -!- PATHWAY: Purine metabolism. {ECO:0000250|UniProtKB:Q9KTX4}.
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; CU468230; CAP02292.1; -; Genomic_DNA.
DR PDB; 4W98; X-ray; 1.43 A; A=1-143.
DR PDB; 4WBF; X-ray; 2.64 A; A=1-140.
DR PDBsum; 4W98; -.
DR PDBsum; 4WBF; -.
DR AlphaFoldDB; B0VKS3; -.
DR SMR; B0VKS3; -.
DR EnsemblBacteria; CAP02292; CAP02292; ABSDF3006.
DR KEGG; abm:ABSDF3006; -.
DR HOGENOM; CLU_060216_8_1_6; -.
DR OMA; KIVAMKM; -.
DR BRENDA; 2.7.4.6; 98.
DR Proteomes; UP000001741; 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..143
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_1000192249"
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:4W98"
FT HELIX 12..16
FT /evidence="ECO:0007829|PDB:4W98"
FT HELIX 20..29
FT /evidence="ECO:0007829|PDB:4W98"
FT STRAND 33..40
FT /evidence="ECO:0007829|PDB:4W98"
FT HELIX 44..50
FT /evidence="ECO:0007829|PDB:4W98"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:4W98"
FT HELIX 60..67
FT /evidence="ECO:0007829|PDB:4W98"
FT STRAND 72..80
FT /evidence="ECO:0007829|PDB:4W98"
FT HELIX 82..90
FT /evidence="ECO:0007829|PDB:4W98"
FT TURN 95..97
FT /evidence="ECO:0007829|PDB:4W98"
FT HELIX 103..107
FT /evidence="ECO:0007829|PDB:4W98"
FT STRAND 109..113
FT /evidence="ECO:0007829|PDB:4WBF"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:4W98"
FT HELIX 122..132
FT /evidence="ECO:0007829|PDB:4W98"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:4W98"
SQ SEQUENCE 143 AA; 15462 MW; 13CBBCF29538FA8D CRC64;
MAIERTLSIV KPDAVSKNHI GEIFARFEKA GLKIVATKMK HLSQADAEGF YAEHKERGFF
GDLVAFMTSG PVVVSVLEGE NAVLAHREIL GATNPKEAAP GTIRADFAVS IDENAAHGSD
SVASAEREIA YFFADNEICP RTR
