ID DNLJ_STRZP Reviewed; 652 AA. AC C1CKI0; DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot. DT 26-MAY-2009, sequence version 1. DT 27-MAR-2024, entry version 82. 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}; GN OrderedLocusNames=SPP_1122; OS Streptococcus pneumoniae (strain P1031). OC Bacteria; Bacillota; Bacilli; Lactobacillales; Streptococcaceae; OC Streptococcus. OX NCBI_TaxID=488223; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=P1031; RX PubMed=21034474; DOI=10.1186/gb-2010-11-10-r107; RA Donati C., Hiller N.L., Tettelin H., Muzzi A., Croucher N.J., RA Angiuoli S.V., Oggioni M., Dunning Hotopp J.C., Hu F.Z., Riley D.R., RA Covacci A., Mitchell T.J., Bentley S.D., Kilian M., Ehrlich G.D., RA Rappuoli R., Moxon E.R., Masignani V.; RT "Structure and dynamics of the pan-genome of Streptococcus pneumoniae and RT closely related species."; RL Genome Biol. 11:R107.1-R107.19(2010). 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; Evidence={ECO:0000255|HAMAP- CC Rule:MF_01588}; CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000255|HAMAP- CC 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; CP000920; ACO21382.1; -; Genomic_DNA. DR RefSeq; WP_001042590.1; NC_012467.1. DR PDB; 4GLW; X-ray; 2.00 A; A/B=1-305. DR PDBsum; 4GLW; -. DR AlphaFoldDB; C1CKI0; -. DR SMR; C1CKI0; -. DR KEGG; spp:SPP_1122; -. DR HOGENOM; CLU_007764_2_1_9; -. 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; 2. 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 1: Evidence at protein level; KW 3D-structure; DNA damage; DNA repair; DNA replication; Ligase; Magnesium; KW Manganese; Metal-binding; NAD; Zinc. FT CHAIN 1..652 FT /note="DNA ligase" FT /id="PRO_0000380487" FT DOMAIN 577..652 FT /note="BRCT" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT ACT_SITE 109 FT /note="N6-AMP-lysine intermediate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 29..33 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 78..79 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 107 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 130 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 164 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 278 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 302 FT /ligand="NAD(+)" FT /ligand_id="ChEBI:CHEBI:57540" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 395 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 398 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 413 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT BINDING 418 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588" FT HELIX 3..6 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 8..12 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 38..45 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 47..49 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 55..58 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 68..71 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 85..95 FT /evidence="ECO:0007829|PDB:4GLW" FT TURN 96..98 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 104..110 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 112..120 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 123..129 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 133..138 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 140..143 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 159..166 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 169..181 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 190..198 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 199..202 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 203..208 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 212..221 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 223..226 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 227..237 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 246..250 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 251..264 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 265..267 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 268..270 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 272..279 FT /evidence="ECO:0007829|PDB:4GLW" FT HELIX 282..288 FT /evidence="ECO:0007829|PDB:4GLW" FT STRAND 292..302 FT /evidence="ECO:0007829|PDB:4GLW" SQ SEQUENCE 652 AA; 72276 MW; C2220D1F3504D47B CRC64; MNKRMNELVA LLNRYATEYY TSDNPSVSDS EYDRLYRELV ELETAYPEQV LADSPTHRVG GKVLDGFEKY SHQYPLYSLQ DAFSREELDA FDARVRKEVA HPTYICELKI DGLSISLTYE KGILVAGVTR GDGSIGENIT ENLKRVKDIP LTLPEELDIT VRGECYMPRA SFDQVNQARQ ENGEPEFANP RNAAAGTLRQ LDTAVVAKRN LATFLYQEAS PSTRDSQEKG LKYLEQLGFV VNPKRILAEN IDEIWNFIQE VGQERENLPY DIDGVVIKVN DLASQEELGF TVKAPKWAVA YKFPAEEKEA QLLSVDWTVG RTGVVTPTAN LTPVQLAGTT VSRATLHNVD YIAEKDIRKD DTVIVYKAGD IIPAVLRVVE SKRVSEEKLD IPTNCPSCNS DLLHFEDEVA LRCINPRCPA QIMEGLIHFA SRDAMNITGL GPSIVEKLFA ANLVKDVADI YRLQEEDFLL LEGVKEKSAA KLYQAIQASK ENSAEKLLFG LGIRHVGSKA SQLLLQYFHS IENLYQADSE EVASIESLGG VIAKSLQTYF ATEGSEILLR ELKETGVNLD YKGQTVVADA ALSGLTVVLT GKLERLKRSE AKSKLESLGA KVTGSVSKKT DLVVVGADAG SKLQKAQELG IQVRDEAWLE SL //