ID A0A7Y5XZ94_9BURK Unreviewed; 690 AA. AC A0A7Y5XZ94; DT 02-JUN-2021, integrated into UniProtKB/TrEMBL. DT 02-JUN-2021, sequence version 1. DT 27-MAR-2024, entry version 11. 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:NUT59772.1}; GN ORFNames=HNO82_01480 {ECO:0000313|EMBL:NUT59772.1}; OS Herbaspirillum sp. C9C3. OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; OC Oxalobacteraceae; Herbaspirillum. OX NCBI_TaxID=2735271 {ECO:0000313|EMBL:NUT59772.1, ECO:0000313|Proteomes:UP000534139}; RN [1] {ECO:0000313|EMBL:NUT59772.1, ECO:0000313|Proteomes:UP000534139} RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=C9C3 {ECO:0000313|EMBL:NUT59772.1, RC ECO:0000313|Proteomes:UP000534139}; RA Nordstedt N.P., Jones M.L.; RT "Isolation of Rhizosphere Bacteria That Improve Quality and Water Stress RT Tolerance in Greenhouse Ornamentals."; RL Front. Plant Sci. 11:0-0(2020). 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:NUT59772.1}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; JABFMQ010000001; NUT59772.1; -; Genomic_DNA. DR AlphaFoldDB; A0A7Y5XZ94; -. DR Proteomes; UP000534139; 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:SF6; REPLICATION FACTOR C SUBUNIT 1; 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|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 606..678 FT /note="BRCT" FT /evidence="ECO:0000259|PROSITE:PS50172" FT ACT_SITE 129 FT /note="N6-AMP-lysine intermediate" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 46..50 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 95..96 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 127 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 150 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 187 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 304 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 328 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 422 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 425 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" FT BINDING 447 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000256|HAMAP-Rule:MF_01588" SQ SEQUENCE 690 AA; 75243 MW; 319DB0554F91BADD CRC64; MQDDLFSAGR PPQGEPDWRA RARTLRDELN RHNHSYYVLD QPSIPDAEYD RLFQQLQALE TAHPELLTPD SPTQRVGAGP LPQFEPVRHD IPMLSLGNGF ADEDIEAFDK RVRDGLETLQ EVRYATELKF DGLAISLRYE NGVLVQAATR GDGTTGENVT ANIRTVRAIP LRLHGDNLPQ VIDVRGEVLM YKEDFARLNQ RQRDAGQKEF ANPRNAAAGS LRQLDSRITA QRTLRFFAYG IGVLEGAEMP PSHSALLDWY QELGLPVCKE RAVVSGAAGL LDFFRSIGAK RESLPYEIDG VVYKVDRLDQ QKHLGFVSRA PRFALAHKFP AQEALTVVQD IEVQVGRTGA ITPVARLNPV FVGGVTVTNA TLHNEDEVRR KDIRIGDTVI VRRAGDVIPE VVAFVPEKRP EDARAFVMPV ACPVCGSPIV RAEEEAVARC SGGWLKCSAQ RKGGLQHFAS RRAMDIEGLG EQLVEQLVDR QVVNTPADLY RLGLSALAEL DRMAEKSAQN VLDALQKSKT TTLARFIYAL GIRHVGEATA KELARHFGGI DKLLAASEEQ LLEVADIGPV VASSIRAFFN DPINVELVEQ LRAVGVHWPE SEGVDAGAKH LAGKTFVLTG TLPNLSRDDA SQMIEAAGGK VSGSVSKKTS YVVAGAEAGS KLAKAEELGV AILDEDALKA LCAGQDVSGT //