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Non-homologous end joining protein Ku (Mt-Ku)

 KU_MYCTU                Reviewed;         273 AA.
P9WKD9; L7N5V9;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
23-FEB-2022, entry version 35.
RecName: Full=Non-homologous end joining protein Ku {ECO:0000255|HAMAP-Rule:MF_01875};
AltName: Full=Mt-Ku;
Name=mku; OrderedLocusNames=Rv0937c;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the complete
genome sequence.";
Nature 393:537-544(1998).
[2]
FUNCTION, INTERACTION WITH LIGD, SUBUNIT, AND DNA-BINDING.
STRAIN=ATCC 25618 / H37Rv;
PubMed=12215643; DOI=10.1126/science.1074584;
Weller G.R., Kysela B., Roy R., Tonkin L.M., Scanlan E., Della M.,
Devine S.K., Day J.P., Wilkinson A., d'Adda di Fagagna F., Devine K.M.,
Bowater R.P., Jeggo P.A., Jackson S.P., Doherty A.J.;
"Identification of a DNA nonhomologous end-joining complex in bacteria.";
Science 297:1686-1689(2002).
[3]
FUNCTION.
STRAIN=ATCC 25618 / H37Rv;
PubMed=15499016; DOI=10.1126/science.1099824;
Della M., Palmbos P.L., Tseng H.M., Tonkin L.M., Daley J.M., Topper L.M.,
Pitcher R.S., Tomkinson A.E., Wilson T.E., Doherty A.J.;
"Mycobacterial Ku and ligase proteins constitute a two-component NHEJ
repair machine.";
Science 306:683-685(2004).
[4]
FUNCTION, INTERACTION WITH LIGD, AND DOMAIN.
PubMed=15778718; DOI=10.1038/nsmb915;
Gong C., Bongiorno P., Martins A., Stephanou N.C., Zhu H., Shuman S.,
Glickman M.S.;
"Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity
repair system driven by Ku, ligase D and ligase C.";
Nat. Struct. Mol. Biol. 12:304-312(2005).
[5]
FUNCTION, AND INTERACTION WITH LIGD.
STRAIN=ATCC 25618 / H37Rv;
PubMed=16023671; DOI=10.1016/j.jmb.2005.06.038;
Pitcher R.S., Tonkin L.M., Green A.J., Doherty A.J.;
"Domain structure of a NHEJ DNA repair ligase from Mycobacterium
tuberculosis.";
J. Mol. Biol. 351:531-544(2005).
[6]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.m111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[7]
INTERACTION WITH SIR2, AND SUBUNIT.
PubMed=21637345; DOI=10.1371/journal.pone.0020045;
Li Z., Wen J., Lin Y., Wang S., Xue P., Zhang Z., Zhou Y., Wang X., Sui L.,
Bi L.J., Zhang X.E.;
"A Sir2-like protein participates in mycobacterial NHEJ.";
PLoS ONE 6:E20045-E20045(2011).
-!- FUNCTION: With LigD forms a non-homologous end joining (NHEJ) repair
enzyme. Binds linear dsDNA with 5'- and 3'-overhangs but not closed
circular dsDNA nor ssDNA. One dimer binds for every 30 bp. Recruits and
stimulates the ligase activity of LigD but not of T4 ligase or a human
ligase complex (LIG4/XRCC4). Attenuates the 3'- to 5'-exonuclease
activity of LigD. Stimulates the template-directed addition of dNTPs by
LigD on 5'-overhangs and nuclease activity on 3'-overhangs.
{ECO:0000269|PubMed:12215643, ECO:0000269|PubMed:15499016,
ECO:0000269|PubMed:15778718, ECO:0000269|PubMed:16023671}.
-!- SUBUNIT: Homodimer (Probable). Interacts with LigD in the absence of
DSBs, and with the isolated Pol domain of LigD in the presence of DNA.
Interacts with Sir2, possibly in a trimeric complex with LigD.
{ECO:0000255|HAMAP-Rule:MF_01875, ECO:0000269|PubMed:12215643,
ECO:0000269|PubMed:15778718, ECO:0000269|PubMed:16023671,
ECO:0000269|PubMed:21637345, ECO:0000305}.
-!- SIMILARITY: Belongs to the prokaryotic Ku family. {ECO:0000255|HAMAP-
Rule:MF_01875}.
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EMBL; AL123456; CCP43685.1; -; Genomic_DNA.
PIR; A70585; A70585.
RefSeq; NP_215452.1; NC_000962.3.
RefSeq; WP_003404795.1; NZ_NVQJ01000001.1.
SMR; P9WKD9; -.
STRING; 83332.Rv0937c; -.
PaxDb; P9WKD9; -.
DNASU; 885050; -.
GeneID; 885050; -.
KEGG; mtu:Rv0937c; -.
TubercuList; Rv0937c; -.
eggNOG; COG1273; Bacteria.
OMA; IRYRKVC; -.
PhylomeDB; P9WKD9; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0033202; C:DNA helicase complex; IDA:MTBBASE.
GO; GO:0003690; F:double-stranded DNA binding; IDA:UniProtKB.
GO; GO:0042803; F:protein homodimerization activity; IPI:MTBBASE.
GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IDA:UniProtKB.
GO; GO:0051351; P:positive regulation of ligase activity; IDA:UniProtKB.
CDD; cd00789; KU_like; 1.
Gene3D; 2.40.290.10; -; 1.
HAMAP; MF_01875; Prokaryotic_Ku; 1.
InterPro; IPR006164; Ku70/Ku80_beta-barrel_dom.
InterPro; IPR009187; Prok_Ku.
InterPro; IPR016194; SPOC-like_C_dom_sf.
PANTHER; PTHR41251; PTHR41251; 1.
Pfam; PF02735; Ku; 1.
PIRSF; PIRSF006493; Prok_Ku; 1.
SMART; SM00559; Ku78; 1.
SUPFAM; SSF100939; SSF100939; 1.
TIGRFAMs; TIGR02772; Ku_bact; 1.
1: Evidence at protein level;
DNA damage; DNA recombination; DNA repair; DNA-binding; Reference proteome.
CHAIN 1..273
/note="Non-homologous end joining protein Ku"
/id="PRO_0000425945"
DOMAIN 10..193
/note="Ku"
/evidence="ECO:0000255|HAMAP-Rule:MF_01875"
REGION 111..273
/note="Sufficient for interaction with LigD"
SEQUENCE 273 AA; 30904 MW; DE11166BC1C52519 CRC64;
MRAIWTGSIA FGLVNVPVKV YSATADHDIR FHQVHAKDNG RIRYKRVCEA CGEVVDYRDL
ARAYESGDGQ MVAITDDDIA SLPEERSREI EVLEFVPAAD VDPMMFDRSY FLEPDSKSSK
SYVLLAKTLA ETDRMAIVHF TLRNKTRLAA LRVKDFGKRE VMMVHTLLWP DEIRDPDFPV
LDQKVEIKPA ELKMAGQVVD SMADDFNPDR YHDTYQEQLQ ELIDTKLEGG QAFTAEDQPR
LLDEPEDVSD LLAKLEASVK ARSKANSNVP TPP


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WP1700: Selenoamino acid metabolism
WP931: G Protein Signaling Pathways
WP1493: Carbon assimilation C4 pathway
WP186: Homologous recombination
WP1153: Homologous recombination
WP346: Protein Modifications

Related Genes :
[ligD Rv0938 MTCY08D9.01c MTCY10D7.36c] Multifunctional non-homologous end joining DNA repair protein LigD (NHEJ DNA repair protein D) (Mt-Lig) (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[mku Rv0937c] Non-homologous end joining protein Ku (Mt-Ku)
[NHEJ1 XLF] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[Nhej1 Xlf] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[ligD MSMEG_5570 MSMEI_5419] Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[ligD PA2138] Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase); DNA ligase D (LigD) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP]); DNA repair polymerase (Pol) (Polymerase/primase)]
[CYREN C7orf49 MRI] Cell cycle regulator of non-homologous end joining (Cell cycle regulator of NHEJ) (Modulator of retrovirus infection homolog)
[XRCC6 G22P1] X-ray repair cross-complementing protein 6 (EC 3.6.4.-) (EC 4.2.99.-) (5'-deoxyribose-5-phosphate lyase Ku70) (5'-dRP lyase Ku70) (70 kDa subunit of Ku antigen) (ATP-dependent DNA helicase 2 subunit 1) (ATP-dependent DNA helicase II 70 kDa subunit) (CTC box-binding factor 75 kDa subunit) (CTC75) (CTCBF) (DNA repair protein XRCC6) (Lupus Ku autoantigen protein p70) (Ku70) (Thyroid-lupus autoantigen) (TLAA) (X-ray repair complementing defective repair in Chinese hamster cells 6)
[YKU80 HDF2 YMR106C YM9718.05C] ATP-dependent DNA helicase II subunit 2 (EC 3.6.4.12) (ATP-dependent DNA helicase II subunit Ku80) (High affinity DNA-binding factor subunit 2) (Yeast Ku80)
[Cyren Mri] Cell cycle regulator of non-homologous end joining (Cell cycle regulator of NHEJ) (Modulator of retrovirus infection homolog)
[mus-51 ku70 NCU08290] ATP-dependent DNA helicase II subunit 1 (EC 3.6.4.12) (ATP-dependent DNA helicase II subunit Ku70) (Protein mus-51)
[ku MSMEG_5580 MSMEI_5431] Non-homologous end joining protein Ku
[YKU70 HDF1 NES24 YMR284W YM8021.10] ATP-dependent DNA helicase II subunit 1 (EC 3.6.4.12) (ATP-dependent DNA helicase II subunit Ku70) (High affinity DNA-binding factor subunit 1)
[ligD BQ2027_MB0963] Multifunctional non-homologous end joining protein LigD (NHEJ DNA polymerase) [Includes: DNA repair polymerase (Pol) (Polymerase/primase); 3'-phosphoesterase (3'-ribonuclease/3'-phosphatase) (PE); DNA ligase (Lig) (EC 6.5.1.1) (Polydeoxyribonucleotide synthase [ATP])]
[nnrE nnrD KU6B_32360] Bifunctional NAD(P)H-hydrate repair enzyme (Nicotinamide nucleotide repair protein) [Includes: ADP-dependent (S)-NAD(P)H-hydrate dehydratase (EC 4.2.1.136) (ADP-dependent NAD(P)HX dehydratase); NAD(P)H-hydrate epimerase (EC 5.1.99.6)]
[Nhej1 Xlf] Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)
[POLY] Genome polyprotein
[POLY] Genome polyprotein
[POLY] Genome polyprotein
[POLY] Genome polyprotein
[mus-52 ku80 NCU00077] ATP-dependent DNA helicase II subunit 2 (EC 3.6.4.12) (ATP-dependent DNA helicase II subunit Ku80) (Protein mus-52)
[pyrG KU43P_11730] CTP synthase (EC 6.3.4.2) (Cytidine 5'-triphosphate synthase) (Cytidine triphosphate synthetase) (CTP synthetase) (CTPS) (UTP--ammonia ligase)
[KU70 KLLA0C06226g] ATP-dependent DNA helicase II subunit 1 (EC 3.6.4.12) (ATP-dependent DNA helicase II subunit Ku70)
[nef] Protein Nef (3'ORF) (Negative factor) (F-protein) [Cleaved into: C-terminal core protein]
[recB KU43P_45870] RecBCD enzyme subunit RecB (EC 3.1.11.5) (Exonuclease V subunit RecB) (ExoV subunit RecB) (Helicase/nuclease RecBCD subunit RecB)
[pyrG KU6B_37200 OA50_00947] CTP synthase (EC 6.3.4.2) (Cytidine 5'-triphosphate synthase) (Cytidine triphosphate synthetase) (CTP synthetase) (CTPS) (UTP--ammonia ligase)
[nef] Protein Nef (3'ORF) (Negative factor) (F-protein) [Cleaved into: C-terminal core protein]
[nef] Protein Nef (3'ORF) (Negative factor) (F-protein) [Cleaved into: C-terminal core protein]
[nef] Protein Nef (3'ORF) (Negative factor) (F-protein) [Cleaved into: C-terminal core protein]
[rbsK KU43P_19730] Ribokinase (RK) (EC 2.7.1.15)

Bibliography :
[27613236] Mycobacterium tuberculosis and Mycobacterium marinum non-homologous end-joining proteins can function together to join DNA ends in Escherichia coli.
[22265216] Persistently bound Ku at DNA ends attenuates DNA end resection and homologous recombination.
[21811007] Mycobacterium tuberculosis Ku can bind to nuclear DNA damage and sensitize mammalian cells to bleomycin sulfate.
[20530153] Characterization of the roles of the catalytic domains of Mycobacterium tuberculosis ligase D in Ku-dependent error-prone DNA end joining.
[17560174] Expression of Mycobacterium tuberculosis Ku and Ligase D in Escherichia coli results in RecA and RecB-independent DNA end-joining at regions of microhomology.
[16023671] Domain structure of a NHEJ DNA repair ligase from Mycobacterium tuberculosis.
[15499016] Mycobacterial Ku and ligase proteins constitute a two-component NHEJ repair machine.