ID A0A087MML4_9GAMM Unreviewed; 707 AA.
AC A0A087MML4;
DT 29-OCT-2014, integrated into UniProtKB/TrEMBL.
DT 29-OCT-2014, sequence version 1.
DT 24-JAN-2024, entry version 47.
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=N788_02760 {ECO:0000313|EMBL:KFL38117.1};
OS Arenimonas donghaensis DSM 18148 = HO3-R19.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Arenimonas.
OX NCBI_TaxID=1121014 {ECO:0000313|EMBL:KFL38117.1, ECO:0000313|Proteomes:UP000029085};
RN [1] {ECO:0000313|Proteomes:UP000029085}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HO3-R19 {ECO:0000313|Proteomes:UP000029085};
RA Chen F., Wang G.;
RT "Genome sequencing of Arenimonas donghaensis.";
RL Submitted (AUG-2013) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:KFL38117.1, ECO:0000313|Proteomes:UP000029085}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HO3-R19 {ECO:0000313|EMBL:KFL38117.1,
RC ECO:0000313|Proteomes:UP000029085};
RX PubMed=26380644; DOI=10.1186/s40793-015-0055-4;
RA Chen F., Wang H., Cao Y., Li X., Wang G.;
RT "High quality draft genomic sequence of Arenimonas donghaensis DSM
RT 18148(T).";
RL Stand. Genomic Sci. 10:59-59(2015).
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:KFL38117.1}.
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DR EMBL; AVCJ01000001; KFL38117.1; -; Genomic_DNA.
DR RefSeq; WP_034220558.1; NZ_AVCJ01000001.1.
DR AlphaFoldDB; A0A087MML4; -.
DR STRING; 1121014.N788_02760; -.
DR PATRIC; fig|1121014.3.peg.526; -.
DR OrthoDB; 9759736at2; -.
DR Proteomes; UP000029085; Unassembled WGS sequence.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-KW.
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 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; 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; 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 Cytoplasm {ECO:0000256|ARBA:ARBA00022490};
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 Reference proteome {ECO:0000313|Proteomes:UP000029085};
KW Zinc {ECO:0000256|ARBA:ARBA00022833, ECO:0000256|HAMAP-Rule:MF_01588}.
FT DOMAIN 625..707
FT /note="BRCT"
FT /evidence="ECO:0000259|PROSITE:PS50172"
FT ACT_SITE 114
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 32..36
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 81..82
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 112
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 135
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 171
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 288
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 312
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 412
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 415
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
FT BINDING 449
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588"
SQ SEQUENCE 707 AA; 76345 MW; 71D3E39187295A6D CRC64;
MSDAAKRIRE LRLALEDANH RYHVLDDPAI PDAEYDAMLR ELQALEQAHP ELGRPDSPTQ
RVGAGVLPGF ETVVHDVPML SLNNAFSDEE VHDFVARISK ELGESEPEFS VEPKLDGLAI
SLRYEDGCFV RGATRGDGAT GEDVTQNLRT VRAIPLRLRG AAPALLEVRG EVYMPRAGFE
AYNARMRESG RKVLANPRNG AAGSLRQLDP KLAAARPLSF YAYGLGATGD WPLPPRHSAV
LQALKGFGFP VSPEVSIARG ADGLLAYYQC IGALRDGLPY DIDGVVYKLD RQDQQKAMGF
VSRAPRWAIA HKFPAQEQTT TVEAIEVQVG RTGALTPVAR LAPVQVAGVT VTNATLHNAD
QIARLDVRVG DTVIVRRAGD VIPEVMRVVD ERRPVDGKGR PLHAPFQFPA QCPACGSHIE
AVRKVLKQTK AGVEYAEGAT LTCTGGLFCP AQRKQALVHF ASRKAMDIDG LGERYIEALV
DFDYVKTVAD LYALQLDDFL EMKRRADERD GTVPETVKAG KVATRWAENL VSAIAASKDT
TLERLLFALG IRDVGESTAR TLARWFGALD PVMAASRESL VEIPDIGPVV AERIAGFFAE
PHNRDVIAAL RAAGVQWPEA GPQRAAEGPL AGKTVVLTGS LSAMSRDEAG NQLQALGAKV
ASSVSKKTDF VVAGEAAGSK LEKATALGIT VWDEARLLAY LNKPEPL
//
