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DNLJ2_NOCFA
ID   DNLJ2_NOCFA             Reviewed;         683 AA.
AC   Q5YRS7;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   03-AUG-2022, entry version 109.
DE   RecName: Full=DNA ligase 2 {ECO:0000255|HAMAP-Rule:MF_01588};
DE            EC=6.5.1.2 {ECO:0000255|HAMAP-Rule:MF_01588};
DE   AltName: Full=Polydeoxyribonucleotide synthase [NAD(+)] 2 {ECO:0000255|HAMAP-Rule:MF_01588};
GN   Name=ligA2 {ECO:0000255|HAMAP-Rule:MF_01588}; OrderedLocusNames=NFA_42650;
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; BAD59114.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q5YRS7; -.
DR   SMR; Q5YRS7; -.
DR   STRING; 247156.NFA_42650; -.
DR   PRIDE; Q5YRS7; -.
DR   EnsemblBacteria; BAD59114; BAD59114; NFA_42650.
DR   KEGG; nfa:NFA_42650; -.
DR   eggNOG; COG0272; Bacteria.
DR   HOGENOM; CLU_007764_2_1_11; -.
DR   OMA; HDVEHEI; -.
DR   Proteomes; UP000006820; 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; Reference proteome; Zinc.
FT   CHAIN           1..683
FT                   /note="DNA ligase 2"
FT                   /id="PRO_0000313343"
FT   DOMAIN          592..681
FT                   /note="BRCT"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   ACT_SITE        108
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         27..31
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         76..77
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         106
FT                   /ligand="NAD(+)"
FT                   /ligand_id="ChEBI:CHEBI:57540"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         129
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         422
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT   BINDING         428
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ   SEQUENCE   683 AA;  74351 MW;  B4311C800344876F CRC64;
     MRWQRLAEEV REHQFRYYVR DAPIISDGEF DALLRELQEL EDRHPDLRTP DSPTQLVGGG
     FATDFTPVDH LERMLSLDNV FDVDELRAWA ARVEAETGPD LHYLCEVKID GVALNLVYER
     GKLVRAATRG DGRTGEDVTL NARTIEDVPG ELSAGGEFPV PELLEVRGEV YLRLADFEAL
     NAAIVAEGKP PYANPRNTAA GSLRQKDPAV TARRRLRMIC HGLGRIEGYT PASQFEAYRA
     LSAWGLPVSE HTRRVRGIDA VIERVAYWGE HRHDIEHEID GQVIKVDETS LQRRLGATSR
     APRWAIAYKY PPEEATTKLR AIEVNVGRTG RVTPFAVMEP VVIAGSTVAM ATLHNASEVK
     RKGVLIGDTV TIRKAGDVIP EVLGPVVDAR TGAEREFVMP THCPECGTEL APEKEGDADI
     RCPNQRSCPA QLRERVYHVA GRSAFDIEAL GYEAAIDLLQ SGAIGDEGDL FDLDEARLLT
     TSLFTNKNGS LSANGKRLLE NLDAAKDRPL WRVLVGLSIR HVGPTAARAL AAEFGSMERI
     EQASVDELAA TDGVGPTIAA AVAEWFTVDW HRAIVAKWRA AGVRMVDERD ESIERTLEGL
     SIVVTGSLQG FSRDGAKEAI LARGGKAAGS VSKKTAFVVV GDAPGAKAAK AEELGVPILD
     EEGFVRLLAE GPAAVAAEEP ESG
 
 
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