ID   DNLJ_SACD2              Reviewed;         674 AA.
AC   Q21JI8;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   18-APR-2006, sequence version 1.
DT   03-AUG-2022, entry version 98.
DE   RecName: Full=DNA ligase {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}; OrderedLocusNames=Sde_1881;
OS   Saccharophagus degradans (strain 2-40 / ATCC 43961 / DSM 17024).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Cellvibrionales;
OC   Cellvibrionaceae; Saccharophagus.
OX   NCBI_TaxID=203122;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=2-40 / ATCC 43961 / DSM 17024;
RX   PubMed=18516288; DOI=10.1371/journal.pgen.1000087;
RA   Weiner R.M., Taylor L.E. II, Henrissat B., Hauser L., Land M.,
RA   Coutinho P.M., Rancurel C., Saunders E.H., Longmire A.G., Zhang H.,
RA   Bayer E.A., Gilbert H.J., Larimer F., Zhulin I.B., Ekborg N.A., Lamed R.,
RA   Richardson P.M., Borovok I., Hutcheson S.;
RT   "Complete genome sequence of the complex carbohydrate-degrading marine
RT   bacterium, Saccharophagus degradans strain 2-40 T.";
RL   PLoS Genet. 4:E1000087-E1000087(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
CC       DNA. {ECO:0000255|HAMAP-Rule:MF_01588}.
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   -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC       subfamily. {ECO:0000255|HAMAP-Rule:MF_01588}.
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DR   EMBL; CP000282; ABD81141.1; -; Genomic_DNA.
DR   RefSeq; WP_011468359.1; NC_007912.1.
DR   AlphaFoldDB; Q21JI8; -.
DR   SMR; Q21JI8; -.
DR   STRING; 203122.Sde_1881; -.
DR   EnsemblBacteria; ABD81141; ABD81141; Sde_1881.
DR   KEGG; sde:Sde_1881; -.
DR   eggNOG; COG0272; Bacteria.
DR   HOGENOM; CLU_007764_2_1_6; -.
DR   OMA; HDVEHEI; -.
DR   OrthoDB; 241401at2; -.
DR   Proteomes; UP000001947; Chromosome.
DR   GO; GO:0003677; F:DNA binding; IEA:InterPro.
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; IPR003583; Hlx-hairpin-Hlx_DNA-bd_motif.
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; SM00278; HhH1; 4.
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   3: Inferred from homology;
KW   DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW   Metal-binding; NAD; Reference proteome; Zinc.
FT   CHAIN           1..674
FT                   /note="DNA ligase"
FT                   /id="PRO_0000313415"
FT   DOMAIN          593..674
FT                   /note="BRCT"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   ACT_SITE        118
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         35..39
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         84..85
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         116
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         139
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         176
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         293
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         317
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         411
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         414
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         435
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ   SEQUENCE   674 AA;  73569 MW;  40C1B121058C8C23 CRC64;
     MAASDAVLDK LESLKNQINY HNKLYYVLDA PELPDAEYDK LFQELQAIEQ QFPELVTEDS
     PTQRVGAAPL DSFASIEHKR PMLSLDNVFN VEELFAFDKR IRDRINADAS LEYSCEPKFD
     GIAASLLYEN GRLKTAATRG DGTVGEDITQ NMRTIGSVPL KLEGNNIPAV LEVRGEVYMP
     KAGFLRINEE ALAKNEKTFV NPRNAAAGSL RQLNPQITAK RPLVFCAYNV GVVEGGELPA
     THYETLTQLF EWGFLVSEER RIAKGIEECE AYYHYLEAKR ESLAYDIDGI VFKVNAFDLQ
     ERLGFVSRAP RWAIAHKFPA QEALTVLHDV EFQVGRTGAI TPVAKLQPIF VGGVTVSNAT
     LHNKDEIERL GIRVGDTVIV RRAGDVIPQI VSIVESKRPQ DAREIKFPTA CPVCGSDVES
     VEGEAAIRCT GGLVCEAQRK ESIKHFASRQ AMDIDGLGDK IVDQLVDNKL VNDVADLYTL
     DIPTLAGLER LGAKSAANLV AAIEASKQTS LDKILYALGI REVGRATARN LANHFCTLNK
     VMDATQEQLI EVTDVGPVVA HYVVDFFAQA NNREVIEKLI AAGVNWPDIE KVDGVKPLEG
     TTYVLTGSLE SLSRDEAKDK LQALGAKVSG SVSAKTTCVV AGPGAGSKLA KAEKLGLAIL
     DEVGLLALLE EHGV