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Database: UniProt/SWISS-PROT
Entry: DNLI_MYCS2
LinkDB: DNLI_MYCS2
Original site: 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   25-OCT-2017, entry version 96.
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   Mycobacterium smegmatis (strain ATCC 700084 / mc(2)155).
OC   Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC   Mycobacterium.
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
RT   orthology 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-
RT   fidelity 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
RT   structure of the broken DNA ends.";
RL   Genes Dev. 22:512-527(2008).
CC   -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA
CC       during DNA replication, DNA recombination and DNA repair.
CC       {ECO:0000255|HAMAP-Rule:MF_00407, ECO:0000269|PubMed:18281464}.
CC   -!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
CC       5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
CC       AMP + diphosphate. {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.
CC       In 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=Translation N-terminally shortened.; Evidence={ECO:0000305};
DR   EMBL; CP000480; ABK74122.1; -; Genomic_DNA.
DR   EMBL; CP001663; AFP38690.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_011728274.1; NZ_CP009494.1.
DR   RefSeq; YP_886629.1; NC_008596.1.
DR   ProteinModelPortal; A0QUP1; -.
DR   SMR; A0QUP1; -.
DR   STRING; 246196.MSMEG_2277; -.
DR   EnsemblBacteria; ABK74122; ABK74122; MSMEG_2277.
DR   EnsemblBacteria; AFP38690; AFP38690; MSMEI_2220.
DR   GeneID; 4536201; -.
DR   KEGG; msg:MSMEI_2220; -.
DR   KEGG; msm:MSMEG_2277; -.
DR   PATRIC; fig|246196.19.peg.2242; -.
DR   eggNOG; ENOG4107RYT; Bacteria.
DR   eggNOG; COG1793; LUCA.
DR   HOGENOM; HOG000036008; -.
DR   KO; K10747; -.
DR   OMA; WLFEESY; -.
DR   OrthoDB; POG091H0BGA; -.
DR   Proteomes; UP000000757; Chromosome.
DR   Proteomes; UP000006158; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR   GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
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:0051103; P:DNA ligation involved in DNA repair; IEA:InterPro.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR   Gene3D; 1.10.3260.10; -; 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; Complete proteome; DNA damage;
KW   DNA recombination; DNA repair; DNA replication; Ligase; Magnesium;
KW   Metal-binding; Nucleotide-binding; Reference proteome.
FT   CHAIN         1    509       DNA ligase B.
FT                                /FTId=PRO_0000365227.
FT   ACT_SITE    214    214       N6-AMP-lysine intermediate.
FT                                {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     212    212       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     219    219       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     234    234       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     263    263       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     299    299       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     371    371       ATP. {ECO:0000255|HAMAP-Rule:MF_00407}.
FT   BINDING     377    377       ATP. {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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