DNLJ_CORDI
ID DNLJ_CORDI Reviewed; 677 AA.
AC Q6NHQ4;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 108.
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=DIP1077;
OS Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype
OS gravis).
OC Bacteria; Actinobacteria; Corynebacteriales; Corynebacteriaceae;
OC Corynebacterium.
OX NCBI_TaxID=257309;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700971 / NCTC 13129 / Biotype gravis;
RX PubMed=14602910; DOI=10.1093/nar/gkg874;
RA Cerdeno-Tarraga A.-M., Efstratiou A., Dover L.G., Holden M.T.G.,
RA Pallen M.J., Bentley S.D., Besra G.S., Churcher C.M., James K.D.,
RA De Zoysa A., Chillingworth T., Cronin A., Dowd L., Feltwell T., Hamlin N.,
RA Holroyd S., Jagels K., Moule S., Quail M.A., Rabbinowitsch E.,
RA Rutherford K.M., Thomson N.R., Unwin L., Whitehead S., Barrell B.G.,
RA Parkhill J.;
RT "The complete genome sequence and analysis of Corynebacterium diphtheriae
RT NCTC13129.";
RL Nucleic Acids Res. 31:6516-6523(2003).
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; BX248357; CAE49600.1; -; Genomic_DNA.
DR RefSeq; WP_010934791.1; NC_002935.2.
DR AlphaFoldDB; Q6NHQ4; -.
DR SMR; Q6NHQ4; -.
DR STRING; 257309.DIP1077; -.
DR PRIDE; Q6NHQ4; -.
DR EnsemblBacteria; CAE49600; CAE49600; DIP1077.
DR KEGG; cdi:DIP1077; -.
DR HOGENOM; CLU_007764_2_1_11; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000002198; 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 3: Inferred from homology;
KW DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW Metal-binding; NAD; Reference proteome; Zinc.
FT CHAIN 1..677
FT /note="DNA ligase"
FT /id="PRO_0000313205"
FT DOMAIN 596..677
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT REGION 189..210
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 112
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 85..86
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 110
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 133
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 173
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 289
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 313
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 407
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 410
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
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 432
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 677 AA; 74766 MW; A3DB72254B796666 CRC64;
MTDNFADLRR QWDDLAEQVR HHRDAYYNHT PEISDAEFDQ LFRQLQQLEQ EHPELAVPES
PTLRVGAPVE QSSFDNVEHL ERMLSLDNVF DAAELDDWLQ RTPSATYLTE LKIDGLSIDL
VYRSGRLERA ATRGDGRVGE DVTANAKVIE DIPHRLQHSD AYPVPELVEI RGEVFIAVED
FALVNEQRQK EGGKPFANPR NAAAGSLRQK DTEAVRKRRL KMICHGIGAS EGFEADTQFD
AYKALEAWGL PVSPYTKRVH SAQEVQERVT YWAQHRHDAT HEMDGLVIKI DSFAEQRALG
STARAPRWAI AYKYPPEEVT TKLLDIQVGV GRTGRVTPFA VMDPVFVAGS TVEMATLHNQ
TEVKRKGVLI GDTVVIRKAG EVIPEVLGPV VEKRDGSERE FIFPTLCPAC GTRLAPQKED
DADWRCPNSQ SCPAQLSSRL TYLAGRGAFD IEALGEKGAE DLIASGVLID EAQLFNLTED
DLKRTKVYTT KAGALNATGE KLLANLESAK HTDLWRVLVA LSIRHVGPTA ARALAVRYRS
LEALRAADVE DIANTEGVGA IIAQSFAQWF DVPWHRNIVE VWADAGVTMA DSEADIPDQV
LEGLTIVVTG SLVDFSRDSA KEAIVSRGGK ASGSVSKKTS YVVVGENAGS KETKARDLGL
RILNEDEFKQ LLANGTV
