ID A0A2T5FV41_9SPHN Unreviewed; 804 AA.
AC A0A2T5FV41;
DT 18-JUL-2018, integrated into UniProtKB/TrEMBL.
DT 18-JUL-2018, sequence version 1.
DT 27-MAR-2024, entry version 21.
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 Name=ligD {ECO:0000313|EMBL:PTQ08579.1};
GN ORFNames=CLG96_15420 {ECO:0000313|EMBL:PTQ08579.1};
OS Sphingomonas oleivorans.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingomonas.
OX NCBI_TaxID=1735121 {ECO:0000313|EMBL:PTQ08579.1, ECO:0000313|Proteomes:UP000244162};
RN [1] {ECO:0000313|EMBL:PTQ08579.1, ECO:0000313|Proteomes:UP000244162}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=FW-11 {ECO:0000313|EMBL:PTQ08579.1,
RC ECO:0000313|Proteomes:UP000244162};
RA Wang L., Chen L.;
RT "Sphingomonas panjinensis sp.nov., isolated from oil-contaminated soil.";
RL Submitted (SEP-2017) 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};
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:PTQ08579.1}.
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DR EMBL; NWBU01000015; PTQ08579.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A2T5FV41; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000244162; Unassembled WGS sequence.
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:PTQ08579.1};
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 Reference proteome {ECO:0000313|Proteomes:UP000244162};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 313..395
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
SQ SEQUENCE 804 AA; 89102 MW; 6423E5B44100CBFD CRC64;
MASSDPLAAY NAKRDFAKTA EPAGKAARGK AGNIFLVQKH DATRLHYDFR LELDGVLKSW
AITRGPSPDP ADKRLAVRTE DHPLAYADFE GTIPKGEYGG GTVMLWDRGT WAPVAGKDPH
ETLEEGHLHF MLDGERMKGE WLLVRMKPRP GEKHENWLLR KVADKHAGAS GALVDRAINS
IATGRTMAEI AEGKKTPAKA RQRRKGNSTA FPAFRPPQLA TLVDSVPTGS GWLHELKYDG
YRCLLAVAGG KAKAYTRTGL DWSDRFAAIV DAATRTIPGS ALIDGEVVAM DEKGHPSFQT
LQNAMKQGGA LRFFAFDLLE QDGEDLTELP NIERKRRLAV LLSNASEPIA YSDHVAGNGE
KLFRELCREG FEGIISKRAD APYRSRRSQA WLKIKCLQRQ EFIIIGWTES ERRSGFRSLL
LGINEHHKLR YAGKVGTGFD SATIAMLTER LRPLERKTPP AEVPRTAARD AHWVKPGLVA
EIAYAEITQD GVLRHPSFLG LREDKPAREV VAEKPQPVLP VMISNPDRII FPEASITKGE
LAAYYARLAD PLLKWLADRP VSLVRCPQGR AKHCFFQRHD AGSFGDRVRQ VMVREKDGKS
EPYLYVDSAE GMLACVQMGT IEFHGWGSKV DAIERPDRMV LDLDPDEGLG FGRVRDAAFH
LRDILAEMGL LSWPMLTGGK GIHVVVPLDA GAEWPAVKDF ASRFAKAIAA AHPERFTANM
KKARRHGRIF LDWMRNQRGA SAILPYAARA RANAPVAAPL SWDELHETDR ASRFTIADAE
ELLDRAGSDA LKDWAVAAQP LPDY
//