DNLJ_STAAU
ID DNLJ_STAAU Reviewed; 667 AA.
AC Q9AIU7;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 115.
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 Staphylococcus aureus.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=1280;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], AND CHARACTERIZATION.
RC STRAIN=NT64;
RX PubMed=11325928; DOI=10.1128/jb.183.10.3016-3024.2001;
RA Kaczmarek F.S., Zaniewski R.P., Gootz T.D., Danley D.E., Mansour M.N.,
RA Griffor M., Kamath A.V., Cronan M., Mueller J., Sun D., Martin P.K.,
RA Benton B., McDowell L., Biek D., Schmid M.B.;
RT "Cloning and functional characterization of an NAD(+)-dependent DNA ligase
RT from Staphylococcus aureus.";
RL J. Bacteriol. 183:3016-3024(2001).
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.
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; AF234833; AAK15020.1; -; Genomic_DNA.
DR RefSeq; WP_000774565.1; NZ_WSFM01000006.1.
DR PDB; 3JSL; X-ray; 1.80 A; A/B=1-312.
DR PDB; 3JSN; X-ray; 1.90 A; A=1-312.
DR PDB; 4CC5; X-ray; 1.88 A; A=1-312.
DR PDB; 4CC6; X-ray; 2.01 A; A=1-312.
DR PDB; 5FPO; X-ray; 1.83 A; A=1-312.
DR PDB; 5FPR; X-ray; 2.00 A; A=1-312.
DR PDBsum; 3JSL; -.
DR PDBsum; 3JSN; -.
DR PDBsum; 4CC5; -.
DR PDBsum; 4CC6; -.
DR PDBsum; 5FPO; -.
DR PDBsum; 5FPR; -.
DR AlphaFoldDB; Q9AIU7; -.
DR SMR; Q9AIU7; -.
DR BindingDB; Q9AIU7; -.
DR ChEMBL; CHEMBL2163181; -.
DR OMA; HDVEHEI; -.
DR BRENDA; 6.5.1.2; 3352.
DR EvolutionaryTrace; Q9AIU7; -.
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; cd00114; LIGANc; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.10190; -; 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; IPR018239; DNA_ligase_AS.
DR InterPro; IPR033136; DNA_ligase_CS.
DR InterPro; IPR001679; DNAligase.
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 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 PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM00278; HhH1; 3.
DR SMART; SM00532; LIGANc; 1.
DR SUPFAM; SSF47781; SSF47781; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 1.
DR TIGRFAMs; TIGR00575; dnlj; 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..667
FT /note="DNA ligase"
FT /id="PRO_0000161762"
FT DOMAIN 586..667
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 112
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 32..36
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 81..82
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 110
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 133
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 167
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 283
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 307
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 401
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 404
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 419
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 424
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT HELIX 5..23
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 32..48
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 50..52
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 58..62
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 72..74
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 83..85
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 88..101
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 107..113
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 115..123
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 126..132
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 136..141
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 143..146
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 162..169
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 172..182
FT /evidence="ECO:0007829|PDB:3JSL"
FT TURN 183..186
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 193..201
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 206..211
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 215..222
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 232..242
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 251..255
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 256..269
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 270..272
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 277..286
FT /evidence="ECO:0007829|PDB:3JSL"
FT HELIX 287..293
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 297..300
FT /evidence="ECO:0007829|PDB:3JSL"
FT STRAND 303..307
FT /evidence="ECO:0007829|PDB:3JSL"
SQ SEQUENCE 667 AA; 75081 MW; F599F7BC8AB59D67 CRC64;
MADLSSRVNE LHDLLNQYSY EYYVEDNPSV PDSEYDKLLH ELIKIEEEHP EYKTVDSPTV
RVGGEAQASF NKVNHDTPML SLGNAFNEDD LRKFDQRIRE QIGNVEYMCE LKIDGLAVSL
KYVDGYFVQG LTRGDGTTGE DITENLKTIH AIPLKMKEPL NVEVRGEAYM PRRSFLRLNE
EKEKNDEQLF ANPRNAAAGS LRQLDSKLTA KRKLSVFIYS VNDFTDFNAR SQSEALDELD
KLGFTTNKNR ARVNNIDGVL EYIEKWTSQR ESLPYDIDGI VIKVNDLDQQ DEMGFTQKSP
RWAIAYKFPA EEVVTKLLDI ELSIGRTGVV TPTAILEPVK VAGTTVSRAS LHNEDLIHDR
DIRIGDSVVV KKAGDIIPEV VRSIPERRPE DAVTYHMPTH CPSCGHELVR IEGEVALRCI
NPKCQAQLVE GLIHFVSRQA MNIDGLGTKI IQQLYQSELI KDVADIFYLT EEDLLPLDRM
GQKKVDNLLA AIQQAKDNSL ENLLFGLGIR HLGVKASQVL AEKYETIDRL LTVTEAELVE
IHDIGDKVAQ SVVTYLENED IRALIQKLKD KHVNMIYKGI KTSDIEGHPE FSGKTIVLTG
KLHQMTRNEA SKWLASQGAK VTSSVTKNTD VVIAGEDAGS KLTKAQSLGI EIWTEQQFVD
KQNELNS
