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DNLI_MYCS2
ID   DNLI_MYCS2              Reviewed;         509 AA.
AC   A0QUP1; I7FAW2;
DT   03-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT   09-JAN-2007, sequence version 1.
DT   03-AUG-2022, entry version 113.
DE   RecName: Full=DNA ligase B;
DE            EC=6.5.1.1 {ECO:0000255|HAMAP-Rule:MF_00407};
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] {ECO:0000255|HAMAP-Rule:MF_00407};
GN   Name=ligB; OrderedLocusNames=MSMEG_2277, MSMEI_2220;
OS   Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (Mycobacterium
OS   smegmatis).
OC   Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC   Mycolicibacterium.
OX   NCBI_TaxID=246196;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700084 / mc(2)155;
RA   Fleischmann R.D., Dodson R.J., Haft D.H., Merkel J.S., Nelson W.C.,
RA   Fraser C.M.;
RL   Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700084 / mc(2)155;
RX   PubMed=17295914; DOI=10.1186/gb-2007-8-2-r20;
RA   Deshayes C., Perrodou E., Gallien S., Euphrasie D., Schaeffer C.,
RA   Van-Dorsselaer A., Poch O., Lecompte O., Reyrat J.-M.;
RT   "Interrupted coding sequences in Mycobacterium smegmatis: authentic
RT   mutations or sequencing errors?";
RL   Genome Biol. 8:R20.1-R20.9(2007).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700084 / mc(2)155;
RX   PubMed=18955433; DOI=10.1101/gr.081901.108;
RA   Gallien S., Perrodou E., Carapito C., Deshayes C., Reyrat J.-M.,
RA   Van Dorsselaer A., Poch O., Schaeffer C., Lecompte O.;
RT   "Ortho-proteogenomics: multiple proteomes investigation through orthology
RT   and a new MS-based protocol.";
RL   Genome Res. 19:128-135(2009).
RN   [4]
RP   DISRUPTION PHENOTYPE.
RC   STRAIN=ATCC 700084 / mc(2)155;
RX   PubMed=15778718; DOI=10.1038/nsmb915;
RA   Gong C., Bongiorno P., Martins A., Stephanou N.C., Zhu H., Shuman S.,
RA   Glickman M.S.;
RT   "Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity
RT   repair system driven by Ku, ligase D and ligase C.";
RL   Nat. Struct. Mol. Biol. 12:304-312(2005).
RN   [5]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=ATCC 700084 / mc(2)155;
RX   PubMed=18281464; DOI=10.1101/gad.1631908;
RA   Aniukwu J., Glickman M.S., Shuman S.;
RT   "The pathways and outcomes of mycobacterial NHEJ depend on the structure of
RT   the broken DNA ends.";
RL   Genes Dev. 22:512-527(2008).
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC       replication, DNA recombination and DNA repair. {ECO:0000255|HAMAP-
CC       Rule:MF_00407, ECO:0000269|PubMed:18281464}.
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:0000255|HAMAP-Rule:MF_00407};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_00407};
CC   -!- DISRUPTION PHENOTYPE: Not essential for growth, no effect on NHEJ. In
CC       quadruple ligB-ligC1-ligC2-ligD deletions NHEJ on blunt and 5'-
CC       overhangs is 0.22 and 0.12% of wild-type respectively; only 4-fold
CC       decrease in 3'-overhang NHEJ. {ECO:0000269|PubMed:15778718,
CC       ECO:0000269|PubMed:18281464}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000255|HAMAP-Rule:MF_00407}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AFP38690.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
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DR   EMBL; CP000480; ABK74122.1; -; Genomic_DNA.
DR   EMBL; CP001663; AFP38690.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; YP_886629.1; NC_008596.1.
DR   AlphaFoldDB; A0QUP1; -.
DR   SMR; A0QUP1; -.
DR   STRING; 246196.MSMEI_2220; -.
DR   EnsemblBacteria; ABK74122; ABK74122; MSMEG_2277.
DR   EnsemblBacteria; AFP38690; AFP38690; MSMEI_2220.
DR   KEGG; msg:MSMEI_2220; -.
DR   KEGG; msm:MSMEG_2277; -.
DR   PATRIC; fig|246196.19.peg.2242; -.
DR   eggNOG; COG1793; Bacteria.
DR   OMA; WLFEESY; -.
DR   Proteomes; UP000000757; Chromosome.
DR   Proteomes; UP000006158; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR   GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR   GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-UniRule.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-UniRule.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-UniRule.
DR   Gene3D; 1.10.3260.10; -; 1.
DR   Gene3D; 2.40.50.140; -; 1.
DR   HAMAP; MF_00407; DNA_ligase; 1.
DR   InterPro; IPR022865; DNA_ligae_ATP-dep_bac/arc.
DR   InterPro; IPR000977; DNA_ligase_ATP-dep.
DR   InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR   InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR   InterPro; IPR016059; DNA_ligase_ATP-dep_CS.
DR   InterPro; IPR012308; DNA_ligase_ATP-dep_N.
DR   InterPro; IPR036599; DNA_ligase_N_sf.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   Pfam; PF04679; DNA_ligase_A_C; 1.
DR   Pfam; PF01068; DNA_ligase_A_M; 1.
DR   Pfam; PF04675; DNA_ligase_A_N; 1.
DR   SUPFAM; SSF117018; SSF117018; 1.
DR   SUPFAM; SSF50249; SSF50249; 1.
DR   TIGRFAMs; TIGR00574; dnl1; 1.
DR   PROSITE; PS00697; DNA_LIGASE_A1; 1.
DR   PROSITE; PS00333; DNA_LIGASE_A2; 1.
DR   PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Cell cycle; Cell division; DNA damage; DNA recombination;
KW   DNA repair; DNA replication; Ligase; Magnesium; Metal-binding;
KW   Nucleotide-binding; Reference proteome.
FT   CHAIN           1..509
FT                   /note="DNA ligase B"
FT                   /id="PRO_0000365227"
FT   ACT_SITE        214
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         212
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         219
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         234
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         263
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         299
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         371
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
FT   BINDING         377
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00407"
SQ   SEQUENCE   509 AA;  54594 MW;  E5C3AADF5B8F311C CRC64;
     MLADVAAAST EVAASSARLV KIERIATLLA RSAAEDDTQA VAVIVSWLSG ELPQRQIGVG
     WAALRTLPPP AATPSLTVDD VDDRLSTIKA VAGKGSQATR AGLVHELFSA ATDPEQKFLR
     HLLSGELRQG ALAGVMADAV AKAAGLPAAE IRRAAMLAGN LPAVAAAAVT GGRAALADFR
     LRVGRPVGPM LAQTATSVDD ALQRLGGTAV LEAKLDGARV QIHRSGCDVS IYTRSLDDVT
     HRLPEVVEAT LALPATELIA DAEAIALRPD GRPHLFQVTA ARFGRKDPGD LGPLSVFFFD
     LLHVDGRDLL DLPTEERFGA LDALVRQDQR VDRLVTTDTV AAQEFLERTL AAGHEGVMAK
     SPHAAYEAGR RGAGWLKVKP VHTLDLVVLA VEWGSGRRQG KLSNIHLGAR DPDSSGFVML
     GKTFKGMTDA MLEWQTQRFL ELADGPTDGY VVHLRPEQVV EIAFDGVQRS SRYPAGMALR
     FVRVLRYRDD KSPAEADTVE TVRRFYERD
 
 
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