DNLJ_KOCRD
ID DNLJ_KOCRD Reviewed; 766 AA.
AC B2GL64;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 10-JUN-2008, sequence version 1.
DT 03-AUG-2022, entry version 87.
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}; OrderedLocusNames=KRH_16730;
OS Kocuria rhizophila (strain ATCC 9341 / DSM 348 / NBRC 103217 / DC2201).
OC Bacteria; Actinobacteria; Micrococcales; Micrococcaceae; Kocuria.
OX NCBI_TaxID=378753;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 9341 / DSM 348 / NBRC 103217 / DC2201;
RX PubMed=18408034; DOI=10.1128/jb.01853-07;
RA Takarada H., Sekine M., Kosugi H., Matsuo Y., Fujisawa T., Omata S.,
RA Kishi E., Shimizu A., Tsukatani N., Tanikawa S., Fujita N., Harayama S.;
RT "Complete genome sequence of the soil actinomycete Kocuria rhizophila.";
RL J. Bacteriol. 190:4139-4146(2008).
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 ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AP009152; BAG30020.1; -; Genomic_DNA.
DR RefSeq; WP_012398741.1; NC_010617.1.
DR AlphaFoldDB; B2GL64; -.
DR SMR; B2GL64; -.
DR STRING; 378753.KRH_16730; -.
DR PRIDE; B2GL64; -.
DR EnsemblBacteria; BAG30020; BAG30020; KRH_16730.
DR KEGG; krh:KRH_16730; -.
DR eggNOG; COG0272; Bacteria.
DR HOGENOM; CLU_007764_2_1_11; -.
DR OMA; HDVEHEI; -.
DR OrthoDB; 241401at2; -.
DR Proteomes; UP000008838; 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..766
FT /note="DNA ligase"
FT /id="PRO_0000380402"
FT DOMAIN 669..758
FT /note="BRCT"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT REGION 1..30
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 747..766
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..23
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 143
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 57..61
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 106..107
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 141
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 164
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 201
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 317
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 341
FT /ligand="NAD(+)"
FT /ligand_id="ChEBI:CHEBI:57540"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 435
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 438
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 454
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
FT BINDING 460
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01588"
SQ SEQUENCE 766 AA; 83591 MW; D62065E42FC111E1 CRC64;
MSTVNAKGAK PATDANGQSL NPEEPSEALR EEYAQLSDRV REARAAYYVH DQPVISDAEY
DQLYRSLEEF EALHPELKAN DSPTQEVGGE VGAAFSPVKH LEKMYSLEDV FSTDELVAWL
ERAQKQVAEL PGAPEVAWLS EVKIDGLAVN LLYRDGVLVR AATRGDGTTG EDITHNVATI
KTIPQRLSGE NLPEEVEVRG EVFISSKDFR TLNEAMVEEG RAPFANPRNA AAGSLRQKDP
QVTARRPLSM FVHGIGYVRG VDLETQSEAY EILRGWGLPV SPYSRVLSTV AEVLEFIAEF
GDKRHALLHE IDGIVVKVDD RRTQFRLGYT SRVPRWAVAY KYPPEEVNTT LVDILVNVGR
TGRVTPFGLM DPVRVAGSTV EMATLHNQDM VRAKGVLIGD TVVLRKAGDV IPEIVGPVVA
LRDGSEREFV MPAECPSCGT PLRPAKEGDV DIRCPNAETC PSQLKERVNH AAGRGAFDIE
ALGEEAARAL TQPVPLDAPD GTELSVPPLR NEAGLFDLTP EDLRDVMVWR DARRTVTDEE
TGEKVQRVTP ELVPYFWTKP TKARPSVPSK TTEQMFAQLE QAKDTELWRV LVALSIRHVG
PTAARSLATS LRSMDAIRQA DPETLAGTDG VGPVIAQAVQ EFFAEPWRRR VVEQWAAAGV
RMEEEVDEST PRTLEGVTVV VTGSLEGYSR DSAKEAILKR GGKASGSVSK KTHFLVAGDN
AGTKLDKAES LGVPVLDEAG FEQLLAQGPE AFGDRADAAD QPAAGE
