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 27-MAR-2024, entry version 121. 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; Actinomycetota; Actinomycetes; Mycobacteriales; 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; Evidence={ECO:0000255|HAMAP- CC 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}; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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.MSMEG_2277; -. DR PaxDb; 246196-MSMEI_2220; -. DR KEGG; msg:MSMEI_2220; -. DR KEGG; msm:MSMEG_2277; -. DR PATRIC; fig|246196.19.peg.2242; -. DR eggNOG; COG1793; Bacteria. DR OrthoDB; 3733803at2; -. 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 CDD; cd07901; Adenylation_DNA_ligase_Arch_LigB; 1. DR CDD; cd07972; OBF_DNA_ligase_Arch_LigB; 1. DR Gene3D; 1.10.3260.10; DNA ligase, ATP-dependent, N-terminal domain; 1. DR Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1. DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 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 NCBIfam; TIGR00574; dnl1; 1. DR PANTHER; PTHR45674; DNA LIGASE 1/3 FAMILY MEMBER; 1. DR PANTHER; PTHR45674:SF13; DNA LIGASE-RELATED; 1. 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; ATP-dependent DNA ligase DNA-binding domain; 1. DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1. DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 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 //