ID A0A1D8YA71_9GAMM Unreviewed; 861 AA.
AC A0A1D8YA71;
DT 15-FEB-2017, integrated into UniProtKB/TrEMBL.
DT 15-FEB-2017, sequence version 1.
DT 27-MAR-2024, entry version 28.
DE RecName: Full=DNA ligase (ATP) {ECO:0000256|ARBA:ARBA00012727};
DE EC=6.5.1.1 {ECO:0000256|ARBA:ARBA00012727};
DE AltName: Full=NHEJ DNA polymerase {ECO:0000256|ARBA:ARBA00029943};
GN ORFNames=BIZ42_09655 {ECO:0000313|EMBL:AOX62448.1};
OS Stenotrophomonas sp. LM091.
OC Bacteria; Pseudomonadota; Gammaproteobacteria; Xanthomonadales;
OC Xanthomonadaceae; Stenotrophomonas.
OX NCBI_TaxID=1904944 {ECO:0000313|EMBL:AOX62448.1, ECO:0000313|Proteomes:UP000177427};
RN [1] {ECO:0000313|EMBL:AOX62448.1, ECO:0000313|Proteomes:UP000177427}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LM091 {ECO:0000313|EMBL:AOX62448.1,
RC ECO:0000313|Proteomes:UP000177427};
RA Lefeuvre P.;
RT "Complete genome sequence of a copper-resistant commensal bacteria:
RT Stenotrophomonas sp. strain LM091.";
RL Submitted (SEP-2016) to the EMBL/GenBank/DDBJ databases.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC diphosphate.; EC=6.5.1.1; Evidence={ECO:0000256|ARBA:ARBA00034003};
CC -!- COFACTOR:
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|ARBA:ARBA00001936};
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DR EMBL; CP017483; AOX62448.1; -; Genomic_DNA.
DR RefSeq; WP_070426298.1; NZ_CP017483.1.
DR AlphaFoldDB; A0A1D8YA71; -.
DR STRING; 1904944.BIZ42_09655; -.
DR KEGG; slm:BIZ42_09655; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000177427; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; IEA:UniProtKB-EC.
DR GO; GO:0003887; F:DNA-directed DNA polymerase activity; IEA:UniProtKB-KW.
DR GO; GO:0004527; F:exonuclease activity; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR CDD; cd07906; Adenylation_DNA_ligase_LigD_LigC; 1.
DR CDD; cd07971; OBF_DNA_ligase_LigD; 1.
DR CDD; cd04862; PaeLigD_Pol_like; 1.
DR Gene3D; 3.30.1490.70; -; 1.
DR Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR Gene3D; 3.90.920.10; DNA primase, PRIM domain; 1.
DR Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 1.
DR InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR InterPro; IPR014146; LigD_ligase_dom.
DR InterPro; IPR014144; LigD_PE_domain.
DR InterPro; IPR014145; LigD_pol_dom.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR014143; NHEJ_ligase_prk.
DR InterPro; IPR033651; PaeLigD_Pol-like.
DR NCBIfam; TIGR02777; LigD_PE_dom; 1.
DR NCBIfam; TIGR02778; ligD_pol; 1.
DR NCBIfam; TIGR02779; NHEJ_ligase_lig; 1.
DR NCBIfam; TIGR02776; NHEJ_ligase_prk; 1.
DR PANTHER; PTHR42705; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING PROTEIN LIGD; 1.
DR PANTHER; PTHR42705:SF2; MULTIFUNCTIONAL NON-HOMOLOGOUS END JOINING DNA REPAIR PROTEIN LIGD; 1.
DR Pfam; PF04679; DNA_ligase_A_C; 1.
DR Pfam; PF01068; DNA_ligase_A_M; 1.
DR Pfam; PF13298; LigD_N; 1.
DR Pfam; PF21686; LigD_Prim-Pol; 1.
DR SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE 4: Predicted;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840};
KW DNA damage {ECO:0000256|ARBA:ARBA00022763};
KW DNA recombination {ECO:0000256|ARBA:ARBA00023172};
KW DNA repair {ECO:0000256|ARBA:ARBA00023204};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW DNA-directed DNA polymerase {ECO:0000256|ARBA:ARBA00022932};
KW Exonuclease {ECO:0000256|ARBA:ARBA00022839};
KW Hydrolase {ECO:0000256|ARBA:ARBA00022801};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000313|EMBL:AOX62448.1};
KW Manganese {ECO:0000256|ARBA:ARBA00023211};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723};
KW Multifunctional enzyme {ECO:0000256|ARBA:ARBA00023268};
KW Nuclease {ECO:0000256|ARBA:ARBA00022722};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741};
KW Nucleotidyltransferase {ECO:0000256|ARBA:ARBA00022695};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 339..432
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 168..218
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 542..577
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 545..560
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 861 AA; 94563 MW; BDD12BA77D727CBC CRC64;
MSLQEYRRKR RFDGTPEPDA ERRGAPARRP IFVVQLHHAS SRHYDFRLEA DGVLKSWAVP
KGPSLRVGEK RLAVEVEDHP LSYATFAGDI PSGHYGAGHV DVYDHGTWAC DGDPLEAIAA
GKVDFVLHGE RLKGGWKLVR TAMKGKQHQW LLIKRDDEEA RDMEADDLLE APPKAGKRAS
AKKVAAANAS KAAPARKTAP AKAATGSPAR KAERKADARW SKRALALQGA RATPYPHDFK
PQLTDHRATA PDGEQWLHEI KWDGYRLLAD VRDGVVSLRS RGGLNWTDDF PEVVQAIERL
PVRDLRLDGE LVVLDAQGRS DFTALQKVID GTAKQPLRYV VFDMPGIAGV DVSRVPLLER
KALLKDLLGA TPGTLAYSDH VRDHGPAVFA ASGEAGFEGI ISKRIDAPYV NARSRDWIKI
KHENTDEFLI VGYTEPKGSR SGFGSLLMAT PDKRGLRYVG RVGTGFDDAA LRALTRQLTP
LTVKDAVVEL PAHVPFTARS VHWVKPVLVA EVAFRGWAKE GLLRQASFKR LREDKHAKDL
GATATAVSPT PSTTAASATP AGTRGRKKAA TAAQDESTVT ISHPERVVFA KAKITKGEVA
DYYRRMARWI LPEVAHRPLS VLRCPDGVDT PCFFQKHHGT GLGGAVKAIP LEQKSGREDY
LYIEDVEGLL QLVQMNTLEL HPWGATVDDP EHPDRLVFDL DPGEGVNWTQ IKAAARDVRA
RLQEAGLESF VRLSGGKGVH VVVPLQPKAD WAQAKDFCEA FAQAMATQAP ERYVATMSKA
KRDGVIFIDW LRNARGATSV SSWSLRARPG AGVAVPLRWE ELGRIAAPDA FPMAKALQRA
ERLKQDPWEG IEQVKQVLPG S
//
