ID DNLJ_GEOSE Reviewed; 670 AA.
AC O87703;
DT 30-MAY-2000, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1998, sequence version 1.
DT 08-NOV-2023, entry version 123.
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}; Synonyms=lig;
OS Geobacillus stearothermophilus (Bacillus stearothermophilus).
OC Bacteria; Bacillota; Bacilli; Bacillales; Bacillaceae; Geobacillus.
OX NCBI_TaxID=1422;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 29609 / DSM 2027 / NCA 1503 / NCIMB 8924;
RX PubMed=10407164; DOI=10.1016/s0167-4838(99)00122-3;
RA Brannigan J.A., Ashford S.R., Doherty A.J., Timson D.J., Wigley D.B.;
RT "Nucleotide sequence, heterologous expression and novel purification of DNA
RT ligase from Bacillus stearothermophilus.";
RL Biochim. Biophys. Acta 1432:413-418(1999).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 1-318, AND ACTIVE SITE.
RX PubMed=10368271; DOI=10.1016/s0969-2126(99)80007-0;
RA Singleton M.R., Hakansson K., Timson D.J., Wigley D.B.;
RT "Structure of the adenylation domain of an NAD+-dependent DNA ligase.";
RL Structure 7:35-42(1999).
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}.
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DR EMBL; AJ011676; CAA09732.1; -; Genomic_DNA.
DR RefSeq; WP_033016671.1; NZ_RCTK01000024.1.
DR PDB; 1B04; X-ray; 2.80 A; A/B=1-318.
DR PDBsum; 1B04; -.
DR AlphaFoldDB; O87703; -.
DR SMR; O87703; -.
DR GeneID; 69834984; -.
DR OrthoDB; 9759736at2; -.
DR BRENDA; 6.5.1.2; 623.
DR EvolutionaryTrace; O87703; -.
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 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..670
FT /note="DNA ligase"
FT /id="PRO_0000161737"
FT DOMAIN 589..670
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 114
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588,
FT ECO:0000305|PubMed:10368271"
FT BINDING 34..38
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 83..84
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 112
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 135
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 169
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 285
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 309
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 403
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 406
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 421
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 426
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT HELIX 3..25
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 35..50
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 52..54
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 60..63
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 92..104
FT /evidence="ECO:0007829|PDB:1B04"
FT STRAND 109..125
FT /evidence="ECO:0007829|PDB:1B04"
FT STRAND 128..134
FT /evidence="ECO:0007829|PDB:1B04"
FT STRAND 141..143
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 145..149
FT /evidence="ECO:0007829|PDB:1B04"
FT STRAND 164..171
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 174..186
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 195..204
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 208..213
FT /evidence="ECO:0007829|PDB:1B04"
FT STRAND 217..223
FT /evidence="ECO:0007829|PDB:1B04"
FT TURN 224..230
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 234..243
FT /evidence="ECO:0007829|PDB:1B04"
FT STRAND 253..257
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 258..271
FT /evidence="ECO:0007829|PDB:1B04"
FT STRAND 279..286
FT /evidence="ECO:0007829|PDB:1B04"
FT HELIX 289..295
FT /evidence="ECO:0007829|PDB:1B04"
FT STRAND 299..301
FT /evidence="ECO:0007829|PDB:1B04"
FT STRAND 305..309
FT /evidence="ECO:0007829|PDB:1B04"
SQ SEQUENCE 670 AA; 74231 MW; B52462314CF9ACF5 CRC64;
MDRQQAERRA AELRELLNRY GYEYYVLDRP SVPDAEYDRL MQELIAIEEQ YPELKTSDSP
TQRIGGPPLE AFRKVAHRVP MMSLANAFGE GDLRDFDRRV RQEVGEAAYV CELKIDGLAV
SVRYEDGYFV QGATRGDGTT GEDITENLKT IRSLPLRLKE PVSLEARGEA FMPKASFLRL
NEERKARGEE LFANPRNAAA GSLRQLDPKV AASRQLDLFV YGLADAEALG IASHSEALDY
LQALGFKVNP ERRRCANIDE VIAFVSEWHD KRPQLPYEID GIVIKVDSFA QQRALGATAK
SPRWAIAYKF PAEEVVTTLI GIEVNVGRTG VVTPTAILEP VRVAGTTVQR ATLHNEDFIR
EKDIRIGDAV IIKKAGDIIP EVVGVVVDRR DGDETPFAMP THCPECESEL VRLEGEVALR
CLNPNCPAQL RERLIHFASR AAMNIEGLGE KVVTQLFNAG LVRDVADLYC LTKEQLVGLE
RMGEKSAANL LAAIEASKQN SLERLLFGLG IRYVGAKAAQ LLAEHFETME RLERATKEEL
MAVPEIGEKM ADAITAFFAQ PEATELLQEL RAYGVNMAYK GPKRSAEAPA DSAFAGKTVV
LTGKLASMSR NEAKEQIERL GGRVTGSVSR STDLVIAGED AGSKLEKAQQ LGIEIWDESR
FLQEINRGKR
//
