DNLJ_RICFE
ID DNLJ_RICFE Reviewed; 689 AA.
AC Q4UN15;
DT 20-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT 20-MAR-2007, sequence version 2.
DT 03-AUG-2022, entry version 93.
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;
GN OrderedLocusNames=RF_0192;
OS Rickettsia felis (strain ATCC VR-1525 / URRWXCal2) (Rickettsia azadi).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rickettsiales;
OC Rickettsiaceae; Rickettsieae; Rickettsia; spotted fever group.
OX NCBI_TaxID=315456;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC VR-1525 / URRWXCal2;
RX PubMed=15984913; DOI=10.1371/journal.pbio.0030248;
RA Ogata H., Renesto P., Audic S., Robert C., Blanc G., Fournier P.-E.,
RA Parinello H., Claverie J.-M., Raoult D.;
RT "The genome sequence of Rickettsia felis identifies the first putative
RT conjugative plasmid in an obligate intracellular parasite.";
RL PLoS Biol. 3:1-12(2005).
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 -!- SEQUENCE CAUTION:
CC Sequence=AAY61043.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; CP000053; AAY61043.1; ALT_INIT; Genomic_DNA.
DR RefSeq; WP_039594843.1; NC_007109.1.
DR AlphaFoldDB; Q4UN15; -.
DR SMR; Q4UN15; -.
DR STRING; 315456.RF_0192; -.
DR EnsemblBacteria; AAY61043; AAY61043; RF_0192.
DR KEGG; rfe:RF_0192; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_5; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000008548; Chromosome.
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; 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; 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 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_0000280947"
FT DOMAIN 610..689
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT ACT_SITE 123
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 40..44
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 89..90
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 121
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 144
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 179
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 295
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 319
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
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 416
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 431
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 437
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 689 AA; 77634 MW; 13C18329860F833A CRC64;
MQNIDLISEE EAKKLLEELA DKIAAYNHAY YIEDNPLVSD SEYDQLFNTN LKLEQKFPHL
VLENSPSKKI GAKITNKFAK ITHQIPMLSL SNAFDEQDVR DFVDRIKNFL RLDEFAPIFC
EPKIDGLSFS AIYKNGLLTT GATRGDGYVG EDITANIKTI KNFPHKIDNA PEFLEVRGEI
YIEKQDFLNL NKEQEEQGRD KFANPRNAAA GSLRQLDASI TAQRSLKYFV YSGGVTEQNL
ASSQEQLLIK LKEFGFSVNE ISKLTNSEEE IFTFYEYLKT NRENLPYEID GVVYKLNDFA
LQNRMGFIAR SPRFATAHKF PAIIGRTKLL SITVQVGRTG TLTPVAELEP IEIGGVTVSR
ATLHNFQEIM RKDVRIDDYV FLQRAGDVIP KITGVDIGKR PNDTIAFDTP LFCPSCNSKL
HYAPEDIIIR CDNGLNCPAQ NYERIRHFVS KNAMDIEGLG RKQVEFLIDK GLISNPLDIF
FLKEKNDSSL TKLENMDGWG KKSVENLFKN IEQSKNVSLP RFIYALGIRH IGEQNAKLLA
REFGSYANFI AQMELLSKND LDIYQKLNDL EGIGDKILVD IIDFFDVKEN TTLIKKLGEV
LNIEDYKETR EQSSLTGKII VFTGSLPTIS RAEAKATAEK LGAKVAASVS SNTDLVVAGV
DAGSKLKKAK ELNIKIIGEE EWLTLIKNV
