DNLJ_NAUPA
ID DNLJ_NAUPA Reviewed; 656 AA.
AC B9L8R4;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 24-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 89.
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=NAMH_0606;
OS Nautilia profundicola (strain ATCC BAA-1463 / DSM 18972 / AmH).
OC Bacteria; Proteobacteria; Epsilonproteobacteria; Nautiliales; Nautiliaceae;
OC Nautilia.
OX NCBI_TaxID=598659;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-1463 / DSM 18972 / AmH;
RX PubMed=19197347; DOI=10.1371/journal.pgen.1000362;
RA Campbell B.J., Smith J.L., Hanson T.E., Klotz M.G., Stein L.Y., Lee C.K.,
RA Wu D., Robinson J.M., Khouri H.M., Eisen J.A., Cary S.C.;
RT "Adaptations to submarine hydrothermal environments exemplified by the
RT genome of Nautilia profundicola.";
RL PLoS Genet. 5:E1000362-E1000362(2009).
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; CP001279; ACM93636.1; -; Genomic_DNA.
DR RefSeq; WP_015902688.1; NC_012115.1.
DR AlphaFoldDB; B9L8R4; -.
DR SMR; B9L8R4; -.
DR STRING; 598659.NAMH_0606; -.
DR PRIDE; B9L8R4; -.
DR EnsemblBacteria; ACM93636; ACM93636; NAMH_0606.
DR KEGG; nam:NAMH_0606; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_7; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000000448; 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; 3.
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..656
FT /note="DNA ligase"
FT /id="PRO_0000380430"
FT DOMAIN 577..656
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 114
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 32..36
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 81..82
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 112
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 135
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 169
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 284
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 402
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 405
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 418
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 423
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 656 AA; 75066 MW; D0AE88BCB1BAF486 CRC64;
MIKDYNDYKK AVDTLKKWAY YYYVLDNPLV TDEEYDKLYH EVEEYEKKHP DKIDPTSPTQ
RVGDVVLEGF EKAKHLSRMW SMEDVFNEKD FLDWVGRVKR ILGHENFSFY IEPKFDGASL
NLIYENGKLI RAETRGDGEI GEDVTLNAKT INSIPLEIKE KSLIEIRGEV VIKKDDFDKL
NEERLKNGEP TFANPRNAAA GSLRQLDPKI TAKRPLIFYP WGVGVNSLNY ERYSELMDYI
YSLGFKEPPK RGVCKDIPCV EKKYDEFVKL RDSFEVMLDG MVVKIDEIKY HDILGYTQKY
PRWMVAYKFP AIEKETIIED VIVQVGRTGV LTPVAVLKPV EIGGVIVERA TLHNFDEIER
MDIRIGDHVI VIRSGDVIPK ITKVLTWKRK GDEKPIPRPT HCPVCGAEVL DEGALIKCQN
LSCPARVVNT IIYFASKNCL DIEGLGESVA KLLYEHGLVK DVTDLFELKV EDLEKLPLFA
RKKAENLVNA IKSKVGVECW RFVNALGIEH IGEVASKKIC EKFGVEFYKH APEEFEEIEG
FGPEMVKSIA EYIRVNKEKI EKLIEILKPK NPEKKEVQKT PFTGKTVVLT GTMSKPRSEI
KKMLEDMGAK VSSSVSKKTD FVIYGEDAGS KYDKAKKLGV NLLSEDDMWK MLKEGK
