ID   F5YT53_MYCSD            Unreviewed;       758 AA.
AC   F5YT53;
DT   27-JUL-2011, integrated into UniProtKB/TrEMBL.
DT   27-JUL-2011, sequence version 1.
DT   27-MAR-2024, entry version 60.
DE   RecName: Full=DNA ligase (ATP) {ECO:0000256|ARBA:ARBA00012727};
DE            EC=6.5.1.1 {ECO:0000256|ARBA:ARBA00012727};
DE   AltName: Full=NHEJ DNA polymerase {ECO:0000256|ARBA:ARBA00029943};
GN   OrderedLocusNames=JDM601_0881 {ECO:0000313|EMBL:AEF34881.1};
OS   Mycolicibacter sinensis (strain JDM601) (Mycobacterium sinense).
OC   Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Mycobacteriaceae;
OC   Mycolicibacter.
OX   NCBI_TaxID=875328 {ECO:0000313|EMBL:AEF34881.1, ECO:0000313|Proteomes:UP000009224};
RN   [1] {ECO:0000313|EMBL:AEF34881.1, ECO:0000313|Proteomes:UP000009224}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=JDM601 {ECO:0000313|EMBL:AEF34881.1,
RC   ECO:0000313|Proteomes:UP000009224};
RX   PubMed=21685274; DOI=10.1128/JB.05291-11;
RA   Zhang Z.Y., Sun Z.Q., Wang Z.L., Wen Z.L., Sun Q.W., Zhu Z.Q., Song Y.Z.,
RA   Zhao J.W., Wang H.H., Zhang S.L., Guo X.K.;
RT   "Complete genome sequence of a novel clinical isolate, the nontuberculous
RT   Mycobacterium strain JDM601.";
RL   J. Bacteriol. 193:4300-4301(2011).
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC         (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC         diphosphate.; EC=6.5.1.1; Evidence={ECO:0000256|ARBA:ARBA00034003};
CC   -!- COFACTOR:
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|ARBA:ARBA00001936};
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DR   EMBL; CP002329; AEF34881.1; -; Genomic_DNA.
DR   RefSeq; WP_013827823.1; NC_015576.1.
DR   AlphaFoldDB; F5YT53; -.
DR   STRING; 875328.JDM601_0881; -.
DR   KEGG; mjd:JDM601_0881; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_2_1_11; -.
DR   OrthoDB; 9802472at2; -.
DR   Proteomes; UP000009224; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
DR   GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR   GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR   CDD; cd07906; Adenylation_DNA_ligase_LigD_LigC; 1.
DR   CDD; cd04863; MtLigD_Pol_like; 1.
DR   CDD; cd07971; OBF_DNA_ligase_LigD; 1.
DR   Gene3D; 3.30.1490.70; -; 1.
DR   Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR   Gene3D; 3.90.920.10; DNA primase, PRIM domain; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR   InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR   InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR   InterPro; IPR014146; LigD_ligase_dom.
DR   InterPro; IPR014144; LigD_PE_domain.
DR   InterPro; IPR014145; LigD_pol_dom.
DR   InterPro; IPR033649; MtLigD_Pol-like.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   NCBIfam; TIGR02777; LigD_PE_dom; 1.
DR   NCBIfam; TIGR02778; ligD_pol; 1.
DR   NCBIfam; TIGR02779; NHEJ_ligase_lig; 1.
DR   PANTHER; PTHR42705; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING PROTEIN LIGD; 1.
DR   PANTHER; PTHR42705:SF2; MULTIFUNCTIONAL NON-HOMOLOGOUS END JOINING DNA REPAIR PROTEIN LIGD; 1.
DR   Pfam; PF04679; DNA_ligase_A_C; 1.
DR   Pfam; PF01068; DNA_ligase_A_M; 1.
DR   Pfam; PF13298; LigD_N; 1.
DR   Pfam; PF21686; LigD_Prim-Pol; 1.
DR   SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE   4: Predicted;
KW   ATP-binding {ECO:0000256|ARBA:ARBA00022840};
KW   DNA damage {ECO:0000256|ARBA:ARBA00022763};
KW   DNA recombination {ECO:0000256|ARBA:ARBA00023172};
KW   DNA repair {ECO:0000256|ARBA:ARBA00023204};
KW   DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW   DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932};
KW   Exonuclease {ECO:0000256|ARBA:ARBA00022839};
KW   Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW   Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000313|EMBL:AEF34881.1};
KW   Manganese {ECO:0000256|ARBA:ARBA00023211};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW   Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW   Nuclease {ECO:0000256|ARBA:ARBA00022722};
KW   Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741};
KW   Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW   Reference proteome {ECO:0000313|Proteomes:UP000009224};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          547..669
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   REGION          733..758
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   758 AA;  83365 MW;  271D73726A939AE0 CRC64;
     MAAQPFQTRV KLTNADKVLY PATGTTKAQV YHYYTRIAEV MLPHIAGRPV TRKRWPNGVA
     QDSFFEKQLA SSAPAWLPRA EVQHRSGITA YPIIDDLDGL AWIAQQAALE VHVPQWRFEA
     EWTGGGRVLK PGPASRLVFD LDPGEGVSMS QLAQVARAIR DLMAELDLDT FPVTSGSKGI
     HVYAALDRPV ASAGAVAVAK RVAQQLESAM PKLVTATMAK KLRAGKVFVD WSQNNASKTT
     IAPYSLRGRD HPTVAAPRSW AELDDPDLRQ LRFDEVLERV EHDGDLLAGL DGPLEGQDRL
     AVYRAKRDAG RTPEPVPAAA PAAGEGNSFV IQEHHARRLH YDFRLERDGV LVSWAVPKNL
     PTTTSVNHLA VRTEDHPLEY GGFEGTIPKG EYGAGTVRIW DSGSYVTEKW QDTSEKGEVI
     VVLRGDRISG RYALIRTGGD QWLAHRMKDQ QTFAFTDLAP MLATHGSVSG LDPKVWAFEG
     KWDGYRLLVE ADRGRVRLRA RSGRDVTGEY PQLQTLAAEL TEHHVVLDGE VVALDAAGVP
     SFAAMQNSAR STRVKFWAFD LLYLDGRPLL RAAYRDRRRL LATLAQGTGL VVKDLLAAGG
     AEALEQSRRL GWEGVIAKKW DSPYQPGRRS PAWVKDKHWR TQEVVIGGWR AGEGARGGGI
     GSLLMGIPEG DGLRFVGRVG TGFTERALAA LKKELTPTDE SPFDAPLPRA DAKGVTFVRP
     TLVGEVRYSE RTADGRLRQP SWRGLRPDKT PDDVVSED
//