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DNLJ1_NOCFA
ID   DNLJ1_NOCFA             Reviewed;         663 AA.
AC   Q5YVN7;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   03-AUG-2022, entry version 112.
DE   RecName: Full=DNA ligase 1 {ECO:0000255|HAMAP-Rule:MF_01588};
DE            EC=6.5.1.2 {ECO:0000255|HAMAP-Rule:MF_01588};
DE   AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] 1 {ECO:0000255|HAMAP-Rule:MF_01588};
GN   Name=ligA1 {ECO:0000255|HAMAP-Rule:MF_01588}; OrderedLocusNames=NFA_29070;
OS   Nocardia farcinica (strain IFM 10152).
OC   Bacteria; Actinobacteria; Corynebacteriales; Nocardiaceae; Nocardia.
OX   NCBI_TaxID=247156;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=IFM 10152;
RX   PubMed=15466710; DOI=10.1073/pnas.0406410101;
RA   Ishikawa J., Yamashita A., Mikami Y., Hoshino Y., Kurita H., Hotta K.,
RA   Shiba T., Hattori M.;
RT   "The complete genomic sequence of Nocardia farcinica IFM 10152.";
RL   Proc. Natl. Acad. Sci. U.S.A. 101:14925-14930(2004).
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; AP006618; BAD57754.1; -; Genomic_DNA.
DR   RefSeq; WP_011209439.1; NC_006361.1.
DR   AlphaFoldDB; Q5YVN7; -.
DR   SMR; Q5YVN7; -.
DR   STRING; 247156.NFA_29070; -.
DR   PRIDE; Q5YVN7; -.
DR   EnsemblBacteria; BAD57754; BAD57754; NFA_29070.
DR   GeneID; 61133630; -.
DR   KEGG; nfa:NFA_29070; -.
DR   eggNOG; COG0272; Bacteria.
DR   HOGENOM; CLU_007764_2_0_11; -.
DR   OMA; GRDQLDI; -.
DR   BioCyc; NFAR247156:NFA_RS14520-MON; -.
DR   Proteomes; UP000006820; Chromosome.
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   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; 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   Pfam; PF01653; DNA_ligase_aden; 1.
DR   Pfam; PF03120; DNA_ligase_OB; 1.
DR   Pfam; PF12826; HHH_2; 1.
DR   PIRSF; PIRSF001604; LigA; 1.
DR   SMART; SM00292; BRCT; 1.
DR   SMART; SM00278; HhH1; 2.
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.
PE   3: Inferred from homology;
KW   DNA damage; DNA repair; DNA replication; Ligase; Magnesium; Manganese;
KW   Metal-binding; NAD; Reference proteome; Zinc.
FT   CHAIN           1..663
FT                   /note="DNA ligase 1"
FT                   /id="PRO_0000313342"
FT   DOMAIN          574..663
FT                   /note="BRCT"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   ACT_SITE        105
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         30..34
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         126
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         294
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         389
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         392
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         407
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         412
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ   SEQUENCE   663 AA;  70584 MW;  42F1C43410049ED0 CRC64;
     MDAGERIREL ADRIVELRTA YYEGAPLVAD AEYDAVEDEL RALIAAHPEL APDPNPLDQV
     GAPAVLHAPV RHSRPMLSLE KATTPEQVAA FFERFPGQPV VVMPKLDGLS LALVYEDGRL
     VRAVTRGDGT TGDDVTMLVR ALVDGVPEQI DVPGRVEVRG EAVMLRSTFL AYNAAHPDKP
     LINPRNAAAG TLRAKDPATV AERRLRFFGF DLDTAEGGAA ADLGEGLRAL GIAGAAMRMC
     ADAEQAQAAI TDIERGRNDL DYDIDGAVLR LADRDAYAAA GTRSNSPRGA LAFKFAAEEK
     TTVLEAVTWD VGKTGKIVPV ARLEPVFVGG TTVTKATLAN QQVIRARDIK VGDTVLVRRA
     GDVIPFVAGV LDASKRTGAE VEIVPPTECP SCGQPVTEQG NSRELFCTNA SCPAQTVRRL
     IHWASRAAAD IDAIGGVWIE RLAEAGILEN PSDFYTLTKE RLLEFDRIGE VSATRMIESI
     DRSRDVGLRR ALIGLAIPMA SEGTAARLAR AGFASLEEVA DAGEERLVAV EDIGPKVAAS
     LVEHLTRLRP ELERLRERGV SLDVREEDLP PVVAAGAPLA GKTVVVTGAI SDPRSGEKVA
     RPTFQRLCEK AGATAASSVS ANTDLLITGA GVGESKLAKA EKLGVEIVDQ ATIWAQLIEA
     KLV
 
 
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