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Entry: A0A1F8H8B1_9BACT
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ID   A0A1F8H8B1_9BACT        Unreviewed;       670 AA.
AC   A0A1F8H8B1;
DT   15-FEB-2017, integrated into UniProtKB/TrEMBL.
DT   15-FEB-2017, sequence version 1.
DT   24-JAN-2024, entry version 24.
DE   RecName: Full=DNA ligase {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
DE            EC=6.5.1.2 {ECO:0000256|HAMAP-Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
DE   AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] {ECO:0000256|HAMAP-Rule:MF_01588};
GN   Name=ligA {ECO:0000256|HAMAP-Rule:MF_01588};
GN   ORFNames=A3I39_02175 {ECO:0000313|EMBL:OGN33109.1};
OS   Candidatus Yanofskybacteria bacterium RIFCSPLOWO2_02_FULL_47_9b.
OC   Bacteria; Candidatus Yanofskybacteria.
OX   NCBI_TaxID=1802708 {ECO:0000313|EMBL:OGN33109.1, ECO:0000313|Proteomes:UP000178155};
RN   [1] {ECO:0000313|EMBL:OGN33109.1, ECO:0000313|Proteomes:UP000178155}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX   PubMed=27774985; DOI=10.1038/ncomms13219;
RA   Anantharaman K., Brown C.T., Hug L.A., Sharon I., Castelle C.J.,
RA   Probst A.J., Thomas B.C., Singh A., Wilkins M.J., Karaoz U., Brodie E.L.,
RA   Williams K.H., Hubbard S.S., Banfield J.F.;
RT   "Thousands of microbial genomes shed light on interconnected biogeochemical
RT   processes in an aquifer system.";
RL   Nat. Commun. 7:13219-13219(2016).
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:0000256|ARBA:ARBA00004067, ECO:0000256|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;
CC         Evidence={ECO:0000256|ARBA:ARBA00034005, ECO:0000256|HAMAP-
CC         Rule:MF_01588, ECO:0000256|RuleBase:RU000618};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
CC       Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_01588};
CC   -!- SIMILARITY: Belongs to the NAD-dependent DNA ligase family. LigA
CC       subfamily. {ECO:0000256|HAMAP-Rule:MF_01588}.
CC   -!- CAUTION: Lacks conserved residue(s) required for the propagation of
CC       feature annotation. {ECO:0000256|HAMAP-Rule:MF_01588}.
CC   -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC       whole genome shotgun (WGS) entry which is preliminary data.
CC       {ECO:0000313|EMBL:OGN33109.1}.
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DR   EMBL; MGKW01000038; OGN33109.1; -; Genomic_DNA.
DR   AlphaFoldDB; A0A1F8H8B1; -.
DR   Proteomes; UP000178155; Unassembled WGS sequence.
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; cd17748; BRCT_DNA_ligase_like; 1.
DR   CDD; cd00114; LIGANc; 1.
DR   Gene3D; 6.20.10.30; -; 1.
DR   Gene3D; 1.10.150.20; 5' to 3' exonuclease, C-terminal subdomain; 2.
DR   Gene3D; 3.40.50.10190; BRCT domain; 1.
DR   Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR   Gene3D; 1.10.287.610; Helix hairpin bin; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 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; IPR001679; DNA_ligase.
DR   InterPro; IPR018239; DNA_ligase_AS.
DR   InterPro; IPR033136; DNA_ligase_CS.
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   NCBIfam; TIGR00575; dnlj; 1.
DR   PANTHER; PTHR23389; CHROMOSOME TRANSMISSION FIDELITY FACTOR 18; 1.
DR   PANTHER; PTHR23389:SF9; DNA LIGASE; 1.
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   Pfam; PF14520; HHH_5; 1.
DR   PIRSF; PIRSF001604; LigA; 1.
DR   SMART; SM00292; BRCT; 1.
DR   SMART; SM00278; HhH1; 4.
DR   SMART; SM00532; LIGANc; 1.
DR   SUPFAM; SSF52113; BRCT domain; 1.
DR   SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   SUPFAM; SSF47781; RuvA domain 2-like; 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 {ECO:0000256|ARBA:ARBA00022763, ECO:0000256|HAMAP-
KW   Rule:MF_01588};
KW   DNA repair {ECO:0000256|ARBA:ARBA00023204, ECO:0000256|HAMAP-
KW   Rule:MF_01588};
KW   DNA replication {ECO:0000256|ARBA:ARBA00022705, ECO:0000256|HAMAP-
KW   Rule:MF_01588};
KW   Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_01588};
KW   Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01588};
KW   Manganese {ECO:0000256|HAMAP-Rule:MF_01588};
KW   Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW   Rule:MF_01588};
KW   NAD {ECO:0000256|ARBA:ARBA00023027, ECO:0000256|HAMAP-Rule:MF_01588};
KW   Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT   DOMAIN          593..670
FT                   /note="BRCT"
FT                   /evidence="ECO:0000259|PROSITE:PS50172"
FT   ACT_SITE        121
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         88..89
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         119
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         142
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         179
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         316
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         410
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         413
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         428
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         433
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ   SEQUENCE   670 AA;  74685 MW;  7A170411BA244F79 CRC64;
     MNKTDAKSRI AKLRKTINHH RYLYHVLDKQ EISEDALDSL KKELFDLEQE FPDLVTADSP
     TQRVGGQPLK EFKKVPHLVA GALVRMNSLN DAFSQEDMRD WLDRVSKTLG QTPSEFYCDL
     KMDGLAVELV YHDGILTQAS TRGDGETGED VTQNIKTIES IPLSLTSEKI PAELVVRGEI
     FLTKKEFTRI NREQSGRSEK IYANPRNLVA GSVRQLDPKI TASRKLSFYG YALMGSDITS
     HSQKCDKLNN FGIPTNPEGK ICKDLAEIQE FYVEIEKQRV ALSYEIDGIV ISINNNLLLE
     RAGIVGKAPR GAVAYKFAPQ EAETIVENIV VQVGRTGTLT PVAFLRPVNV GGVMVSRATL
     HNLDEIKRLR VKIGDTVIVG RAGDVIPDVK KVLVELRTGK EKEFRMPLRC PACGEKIVQM
     EGQVAYKCVN QDCPAIKREA IYHFVSRKAL DMDGIGPKII DQLMDVALIK DVADLYTLKK
     EDLLNLDRFA EISAGNAIDS IHARKSVPLS RFIYALGIPH VGEETAFTLA KRFGTFEKFR
     LASQSELQAI EDIGPVVSDS ISNWFSHAYN KKLLEKFKGS GLKIENEKIV RQLADRKLEG
     KTFVLTGTLE SLSRDQAKER IREQGGDVSS SVSKETDFVV AGAEPGSKYD KAEKLGVKIL
     DEKEFLKLLG
//
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