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Database: UniProt
Entry: D3LT85_9FIRM
LinkDB: D3LT85_9FIRM
Original site: D3LT85_9FIRM 
ID   D3LT85_9FIRM            Unreviewed;       668 AA.
AC   D3LT85;
DT   20-APR-2010, integrated into UniProtKB/TrEMBL.
DT   20-APR-2010, sequence version 1.
DT   24-JAN-2024, entry version 75.
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   ECO:0000313|EMBL:EFD94655.1};
GN   ORFNames=HMPREF0889_0071 {ECO:0000313|EMBL:EFD94655.1};
OS   Megasphaera genomosp. type_1 str. 28L.
OC   Bacteria; Bacillota; Negativicutes; Veillonellales; Veillonellaceae;
OC   Megasphaera.
OX   NCBI_TaxID=699218 {ECO:0000313|EMBL:EFD94655.1, ECO:0000313|Proteomes:UP000003242};
RN   [1] {ECO:0000313|Proteomes:UP000003242}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=28L {ECO:0000313|Proteomes:UP000003242};
RA   Madupu R., Durkin A.S., Torralba M., Methe B., Sutton G.G.,
RA   Strausberg R.L., Nelson K.E.;
RT   "Sequence of Clostridiales genomosp. BVAB3 str. UPII9-5.";
RL   Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases.
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: 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:EFD94655.1}.
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DR   EMBL; ADGP01000008; EFD94655.1; -; Genomic_DNA.
DR   RefSeq; WP_009369470.1; NZ_ADGP01000008.1.
DR   AlphaFoldDB; D3LT85; -.
DR   STRING; 699218.HMPREF0889_0071; -.
DR   eggNOG; COG0272; Bacteria.
DR   OrthoDB; 9759736at2; -.
DR   Proteomes; UP000003242; 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; 3.
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|ARBA:ARBA00023211, 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          589..668
FT                   /note="BRCT"
FT                   /evidence="ECO:0000259|PROSITE:PS50172"
FT   ACT_SITE        118
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         36..40
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         85..86
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         116
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         139
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         174
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         290
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         314
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         408
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         411
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         426
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT   BINDING         431
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ   SEQUENCE   668 AA;  73930 MW;  6FFA9029F4D14493 CRC64;
     MTKREEQEKV RLAEIKKQLA ELSYQYYTLD APTVSDYEYD MLYRELETLE KKYPQWVTPD
     SPTQRIGSKI SGTFAKYTHD RPMLSLGDVF SDEEVREFDA RVRQELPGER VAYVVELKID
     GLAVNLIYEK GRFVRGVTRG DGHVGEDITH NVRTIRTVPL HISDLSDHVE IRGEVYMPIP
     AFRALNEQRS ADELEPFANP RNAAAGSLRQ QDPQVAAERK LSFFAYALGG TSDWRPESQE
     ALLQTLRNLH FPVNREYRTF TDIQDVIAYI HTWDTRRDTL SYATDGMVIK VNSFAQQQML
     GNTVKIPRWA IAYKFPPEQA RTKVLQIRVG VGRTGVLTPT AELQPVRLAG TTVKSATLHN
     EEYIRSKDIR IGDTVLIQKA GEIIPEVVRP VMEARTGREV VFVMPTQCPS CGGQVQREAG
     EAAVRCVNPA CPAMVAEQIA HFVSRPAMNI EGLGTAIVKQ LIDHGLIHDV ADLFLLHKEE
     ILPLEGFGEK SADNLLQSIA AAKEAGLGRL LFALGIRFVG AKAGRILAET FGSMQALAAA
     DIATLMAVET IGPRIAESVA AYFADSQKVR VIQKLAAAGV GMTEKKRQLI NTSFDGEIVV
     LTGKLQHFSR KEAEAAISAR GGSCTATVTK KTTLVVCGAD PGSKYDKAKA LGTPTIGEEE
     FCDRLNRE
//
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