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 27-MAR-2024, entry version 117.
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; Actinomycetota; Actinomycetes; Mycobacteriales; Nocardiaceae;
OC 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 RefSeq; WP_050768315.1; NC_006361.1.
DR AlphaFoldDB; Q5YRS7; -.
DR SMR; Q5YRS7; -.
DR STRING; 247156.NFA_42650; -.
DR GeneID; 61134895; -.
DR KEGG; nfa:NFA_42650; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_11; -.
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; 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; 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 PIRSF; PIRSF001604; LigA; 1.
DR SMART; SM00292; BRCT; 1.
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 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
//
