ID DNLJ_METI4 Reviewed; 689 AA. AC B3DWU2; DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot. DT 22-JUL-2008, sequence version 1. DT 29-MAY-2024, entry version 91. 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=Minf_1701; OS Methylacidiphilum infernorum (isolate V4) (Methylokorus infernorum (strain OS V4)). OC Bacteria; Verrucomicrobiota; Methylacidiphilae; Methylacidiphilales; OC Methylacidiphilaceae; Methylacidiphilum (ex Ratnadevi et al. 2023). OX NCBI_TaxID=481448; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=Isolate V4; RX PubMed=18593465; DOI=10.1186/1745-6150-3-26; RA Hou S., Makarova K.S., Saw J.H., Senin P., Ly B.V., Zhou Z., Ren Y., RA Wang J., Galperin M.Y., Omelchenko M.V., Wolf Y.I., Yutin N., Koonin E.V., RA Stott M.B., Mountain B.W., Crowe M.A., Smirnova A.V., Dunfield P.F., RA Feng L., Wang L., Alam M.; RT "Complete genome sequence of the extremely acidophilic methanotroph isolate RT V4, Methylacidiphilum infernorum, a representative of the bacterial phylum RT Verrucomicrobia."; RL Biol. Direct 3:26-26(2008). 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}. 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; CP000975; ACD83755.1; -; Genomic_DNA. DR AlphaFoldDB; B3DWU2; -. DR SMR; B3DWU2; -. DR STRING; 481448.Minf_1701; -. DR KEGG; min:Minf_1701; -. DR eggNOG; COG0272; Bacteria. DR HOGENOM; CLU_007764_2_1_0; -. DR OrthoDB; 9759736at2; -. DR Proteomes; UP000009149; Chromosome. DR GO; GO:0005829; C:cytosol; IEA:TreeGrafter. 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:0006288; P:base-excision repair, DNA ligation; IEA:TreeGrafter. 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; 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 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; DNA repair; DNA replication; Ligase; Magnesium; Manganese; KW Metal-binding; NAD; Zinc. FT CHAIN 1..689 FT /note="DNA ligase" FT /id="PRO_0000380416" FT DOMAIN 611..689 FT /note="BRCT" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT ACT_SITE 140 FT /note="N6-AMP-lysine intermediate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 58..62 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 107..108 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 138 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 161 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 198 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 314 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 338 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 432 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 435 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 448 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 453 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" SQ SEQUENCE 689 AA; 77418 MW; A067A22CB46CB6DE CRC64; MIESYLAFIF LNKVNKKKAP SLDSLGYEEI KKRHDELVKL IRKYDYAYYV EAHPLVSDQE YDNLYHELET LEKLHPELIT PDSPTQRIGE TPLSGFSQVT HEIPMLSLEN TYSKEELFAF LERIKRALPG KKISFTVEPK IDGVSISAVY KNGLFSLGAT RGNGTVGDDI TQNLKTIRSL PLRLETPDPP EYLEVRGEAY MSPKDFERLN AQREKEGKVL FANPRNATAG SLKQLDPRVV AERPLAVVFY GAGKLVGMKC KTQEEWLNFL KKIGLPIPIV FWVCSNENEV YEAIGKLNEC RNQLPYPTDG AAVKVNEWEY YSLLGYTAKA PRWAFAYKYG AERAKTRLNN VIFQVGRSGT ITPVAEMDPV FLSGTTVSRA TLHNFDQVKR LDVKIGDVVY LEKAGEVIPE VVGVDLNQRR GTEKEIVPPE FCPSCGEKLS WEGIFLRCEN ENCPAQLKER ILHFAQRNAM DIQGLGESLV DQLVDKGIVK DVADIYDLDE ETLVNLDRMG KKSAQNLLKA IEESKKKDLS RLIFGLGIPH IGQKASEDLA RYFGTMDKLS HATEEELLNL PFIGEIMARS IVNYFRKEAN RRRLEKLRKK GLNFVSTLSQ ASSGTLSGKT FVITGTLSEP RESIAQKIIS KGGRVSNSLS RKTSYLVVGS DPGSKLQEAK KLGIPLINEQ ELLEMLHGG //