DNLJ_MYCS2
ID DNLJ_MYCS2 Reviewed; 701 AA.
AC A0QUW7; I7FZU4;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 09-JAN-2007, sequence version 1.
DT 03-AUG-2022, entry version 108.
DE RecName: Full=DNA ligase A {ECO:0000255|HAMAP-Rule:MF_01588};
DE EC=6.5.1.2 {ECO:0000255|HAMAP-Rule:MF_01588};
DE AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000255|HAMAP-Rule:MF_01588};
GN Name=ligA {ECO:0000255|HAMAP-Rule:MF_01588};
GN OrderedLocusNames=MSMEG_2362, MSMEI_2302;
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], AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
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 catalyzes the formation of phosphodiester
CC linkages between 5'-phosphoryl and 3'-hydroxyl groups in double-
CC stranded DNA using NAD as a coenzyme and as the energy source for the
CC reaction. It is essential for DNA replication and repair of damaged DNA
CC (Probable). Probably the only ligase required for non-homologous end
CC joining (NHEJ) repair of 3-overhangs. {ECO:0000255|HAMAP-Rule:MF_01588,
CC ECO:0000269|PubMed:18281464, ECO:0000305}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta-
CC nicotinamide D-nucleotide.; EC=6.5.1.2; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01588};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01588};
CC -!- DISRUPTION PHENOTYPE: Essential, it cannot be disrupted.
CC {ECO:0000269|PubMed:15778718, ECO:0000269|PubMed:18281464}.
CC -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC subfamily. {ECO:0000255|HAMAP-Rule:MF_01588}.
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DR EMBL; CP000480; ABK72497.1; -; Genomic_DNA.
DR EMBL; CP001663; AFP38772.1; -; Genomic_DNA.
DR RefSeq; WP_011728295.1; NZ_SIJM01000012.1.
DR RefSeq; YP_886705.1; NC_008596.1.
DR AlphaFoldDB; A0QUW7; -.
DR SMR; A0QUW7; -.
DR STRING; 246196.MSMEI_2302; -.
DR EnsemblBacteria; ABK72497; ABK72497; MSMEG_2362.
DR EnsemblBacteria; AFP38772; AFP38772; MSMEI_2302.
DR GeneID; 66733776; -.
DR KEGG; msg:MSMEI_2302; -.
DR KEGG; msm:MSMEG_2362; -.
DR PATRIC; fig|246196.19.peg.2328; -.
DR eggNOG; COG0272; Bacteria.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000000757; Chromosome.
DR Proteomes; UP000006158; Chromosome.
DR GO; GO:0003911; F:DNA ligase (NAD+) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR CDD; cd00114; LIGANc; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.10190; -; 1.
DR HAMAP; MF_01588; DNA_ligase_A; 1.
DR InterPro; IPR001357; BRCT_dom.
DR InterPro; IPR036420; BRCT_dom_sf.
DR InterPro; IPR041663; DisA/LigA_HHH.
DR InterPro; IPR018239; DNA_ligase_AS.
DR InterPro; IPR033136; DNA_ligase_CS.
DR InterPro; IPR001679; DNAligase.
DR InterPro; IPR013839; DNAligase_adenylation.
DR InterPro; IPR013840; DNAligase_N.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR004150; NAD_DNA_ligase_OB.
DR InterPro; IPR010994; RuvA_2-like.
DR InterPro; IPR004149; Znf_DNAligase_C4.
DR Pfam; PF00533; BRCT; 1.
DR Pfam; PF01653; DNA_ligase_aden; 1.
DR Pfam; PF03120; DNA_ligase_OB; 1.
DR Pfam; PF03119; DNA_ligase_ZBD; 1.
DR Pfam; PF12826; HHH_2; 1.
DR PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM00532; LIGANc; 1.
DR SUPFAM; SSF47781; SSF47781; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 1.
DR TIGRFAMs; TIGR00575; dnlj; 1.
DR PROSITE; PS50172; BRCT; 1.
DR PROSITE; PS01055; DNA_LIGASE_N1; 1.
DR PROSITE; PS01056; DNA_LIGASE_N2; 1.
PE 1: Evidence at protein level;
KW DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW Metal-binding; NAD; Reference proteome; Zinc.
FT CHAIN 1..701
FT /note="DNA ligase A"
FT /id="PRO_0000313312"
FT DOMAIN 615..701
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT REGION 1..23
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 131
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 49..53
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 99..100
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 129
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 152
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 192
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 308
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 332
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 426
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 429
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 445
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 451
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 701 AA; 76269 MW; 3A37884B5D1DF931 CRC64;
MSEKATGEVE AELPEHPDAD ERRRWQELAD EVREHQFRYY VKDAPIISDA EFDKLLRELQ
ALEDAHPELR TPDSPTQLVG GAGFATEFAP AEHLERMLSL DNVFDSDELT AWAARISSET
GDAAHFLCEL KIDGVALSLV YRDGRLERGA TRGDGRTGED VTLNARTIDD IPERLTPSDE
FPVPAVLEVR GEVFFRVADF EELNAGLVAE GKPPFANPRN SAAGSLRQKN PAVTARRKLR
MICHGIGYTE GFTPASLHDA YRALGAWGLP VSEHTTKVST VAEVAERIAY WGEHRHDVEH
EIDGVVVKVD EVALQRRLGA TSRAPRWAVA YKYPPEEATT KLLDIRVNVG RTGRVTPFAY
MEPVKVAGST VGLATLHNAS EVKRKGVLIG DTVVIRKAGD VIPEVLGPVV DLRDGTEREF
EFPTHCPECG TELAPAKEGD ADIRCPNSRS CPAQLRERLF HLAGRGAFDI EGLGYEAATA
LLAAQVIPDE GDLFTLTADD LLRTELFTTK KGELSANGKR LLANLTKAKE QPLWRVLVAL
SIRHVGPTAA RALATEFGSL EAIEAASEEE LAAVEGVGPT IAAAVKDWFT VDWHRAIVDK
WRAAGVRMAD ERDASIERTL EGLSIVVTGS LAGFSRDQAK EAIIARGGKA AGSVSKKTAY
VVAGDAPGSK YDKAVELGVP VLDEDGFRRL LEQGPPVEPA E
