NDK_MYCTU
ID NDK_MYCTU Reviewed; 136 AA.
AC P9WJH7; L0TCD2; P71904; P84284;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 43.
DE RecName: Full=Nucleoside diphosphate kinase {ECO:0000255|HAMAP-Rule:MF_00451};
DE Short=NDK {ECO:0000255|HAMAP-Rule:MF_00451};
DE Short=NDKA;
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=ndkA; Synonyms=ndk; OrderedLocusNames=Rv2445c;
GN ORFNames=MTCY428.01, MTV008.01c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), AND SUBUNIT.
RX PubMed=12001234; DOI=10.1002/prot.10113.abs;
RA Chen Y., Morera S., Mocan J., Lascu I., Janin J.;
RT "X-ray structure of Mycobacterium tuberculosis nucleoside diphosphate
RT kinase.";
RL Proteins 47:556-557(2002).
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: Homohexamer. {ECO:0000269|PubMed:12001234}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00451}.
CC -!- SIMILARITY: Belongs to the NDK family. {ECO:0000255|HAMAP-
CC Rule:MF_00451, ECO:0000305}.
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DR EMBL; AL123456; CCP45238.1; -; Genomic_DNA.
DR PIR; C70681; C70681.
DR RefSeq; NP_216961.1; NC_000962.3.
DR RefSeq; WP_003412592.1; NZ_NVQJ01000024.1.
DR PDB; 1K44; X-ray; 2.60 A; A/B/C/D/E/F=1-136.
DR PDB; 4ANC; X-ray; 2.80 A; A=1-136.
DR PDB; 4AND; X-ray; 2.81 A; A/B=1-136.
DR PDB; 4ANE; X-ray; 1.90 A; A/B/C/D/E/F=1-136.
DR PDBsum; 1K44; -.
DR PDBsum; 4ANC; -.
DR PDBsum; 4AND; -.
DR PDBsum; 4ANE; -.
DR AlphaFoldDB; P9WJH7; -.
DR SMR; P9WJH7; -.
DR STRING; 83332.Rv2445c; -.
DR PaxDb; P9WJH7; -.
DR DNASU; 885905; -.
DR GeneID; 45426435; -.
DR GeneID; 885905; -.
DR KEGG; mtu:Rv2445c; -.
DR TubercuList; Rv2445c; -.
DR eggNOG; COG0105; Bacteria.
DR OMA; KIVAMKM; -.
DR PhylomeDB; P9WJH7; -.
DR BRENDA; 2.7.4.6; 3445.
DR Reactome; R-HSA-9636383; Prevention of phagosomal-lysosomal fusion.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005829; C:cytosol; TAS:Reactome.
DR GO; GO:0005576; C:extracellular region; HDA:MTBBASE.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0004518; F:nuclease activity; IDA:MTBBASE.
DR GO; GO:0004550; F:nucleoside diphosphate kinase activity; IBA:GO_Central.
DR GO; GO:0004721; F:phosphoprotein phosphatase activity; TAS:Reactome.
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:0090305; P:nucleic acid phosphodiester bond hydrolysis; IDA:MTBBASE.
DR GO; GO:0006165; P:nucleoside diphosphate phosphorylation; IEA:InterPro.
DR GO; GO:0046777; P:protein autophosphorylation; IDA:MTBBASE.
DR GO; GO:0006163; P:purine nucleotide metabolic process; IBA:GO_Central.
DR GO; GO:0006220; P:pyrimidine nucleotide metabolic process; IBA:GO_Central.
DR GO; GO:0052170; P:suppression by symbiont of host innate immune response; TAS:Reactome.
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 Pfam; PF00334; NDK; 1.
DR PRINTS; PR01243; NUCDPKINASE.
DR SMART; SM00562; NDK; 1.
DR SUPFAM; SSF54919; SSF54919; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Kinase; Magnesium; Metal-binding;
KW Nucleotide metabolism; Nucleotide-binding; Reference proteome; Transferase.
FT CHAIN 1..136
FT /note="Nucleoside diphosphate kinase"
FT /id="PRO_0000137010"
FT ACT_SITE 117
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 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 4..9
FT /evidence="ECO:0007829|PDB:4ANE"
FT HELIX 11..15
FT /evidence="ECO:0007829|PDB:4ANE"
FT HELIX 19..28
FT /evidence="ECO:0007829|PDB:4ANE"
FT STRAND 32..39
FT /evidence="ECO:0007829|PDB:4ANE"
FT HELIX 43..49
FT /evidence="ECO:0007829|PDB:4ANE"
FT HELIX 51..53
FT /evidence="ECO:0007829|PDB:4ANE"
FT STRAND 54..56
FT /evidence="ECO:0007829|PDB:4AND"
FT HELIX 59..66
FT /evidence="ECO:0007829|PDB:4ANE"
FT STRAND 71..78
FT /evidence="ECO:0007829|PDB:4ANE"
FT HELIX 81..89
FT /evidence="ECO:0007829|PDB:4ANE"
FT TURN 94..97
FT /evidence="ECO:0007829|PDB:4ANE"
FT HELIX 103..107
FT /evidence="ECO:0007829|PDB:4ANE"
FT HELIX 111..113
FT /evidence="ECO:0007829|PDB:4ANE"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:4ANE"
FT HELIX 122..132
FT /evidence="ECO:0007829|PDB:4ANE"
SQ SEQUENCE 136 AA; 14508 MW; E59E558D514F8CCD CRC64;
MTERTLVLIK PDGIERQLIG EIISRIERKG LTIAALQLRT VSAELASQHY AEHEGKPFFG
SLLEFITSGP VVAAIVEGTR AIAAVRQLAG GTDPVQAAAP GTIRGDFALE TQFNLVHGSD
SAESAQREIA LWFPGA
