ID A0A1B3MN47_9SPHN Unreviewed; 833 AA.
AC A0A1B3MN47;
DT 02-NOV-2016, integrated into UniProtKB/TrEMBL.
DT 02-NOV-2016, sequence version 1.
DT 27-MAR-2024, entry version 37.
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:AOF94518.1};
GN ORFNames=BSY17_3243 {ECO:0000313|EMBL:AOF94518.1};
OS Sphingobium sp. RAC03.
OG Plasmid pbsy17_1 {ECO:0000313|Proteomes:UP000094323}.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingobium.
OX NCBI_TaxID=1843368 {ECO:0000313|EMBL:AOF94518.1, ECO:0000313|Proteomes:UP000094323};
RN [1] {ECO:0000313|EMBL:AOF94518.1, ECO:0000313|Proteomes:UP000094323}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RAC03 {ECO:0000313|EMBL:AOF94518.1,
RC ECO:0000313|Proteomes:UP000094323};
RC PLASMID=pbsy17_1 {ECO:0000313|Proteomes:UP000094323};
RA Fixen K.R., Hovde B., Kunde Y.A., Davenport K.W., Johnson S.L., Li P.-E.,
RA Xu Y., Daligault H.E., Deodato C.R., Starkenburg S.R., Cattolico R.A.;
RL Submitted (JUL-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; CP016453; AOF94518.1; -; Genomic_DNA.
DR RefSeq; WP_069063917.1; NZ_CP016453.1.
DR AlphaFoldDB; A0A1B3MN47; -.
DR KEGG; sphr:BSY17_3243; -.
DR PATRIC; fig|1843368.3.peg.3314; -.
DR Proteomes; UP000094323; Plasmid pbsy17_1.
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:AOF94518.1};
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 Plasmid {ECO:0000313|EMBL:AOF94518.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000094323};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 333..415
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 199..232
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 833 AA; 91587 MW; 3EC2196152D63AC7 CRC64;
MTRTQTKSAD ESLAIYRAKR DFGRTAEPSG AKLPSTGNGF VVQKHAATRL HYDFRLELDG
VLVSWAITRG PSVNPDDKRL AVRTEDHPLD YARFEGTIPK GEYGGGTVML WDNGTWESIP
GKDPRETLPE GHLHFILHGR RMAGEWILFR LKPRGKEKGE NWILRKVNDA FAGGSDDLVG
IHLTSVDTGR TMDEIATGKA VPKRKGAKPA ASPSAASAKP FGKRKKAGTP PPFQPVQLAA
LVDHVPSGDR WIHELKYDGY RTLLAIGGGE GRAYTRSGLD WSDRFAGLIG DAVTLDVASA
LIDGEAVVIM PDGRTSFQAL QAALKGDPGK IDYVAFDLLE LDGEDLTQRP LLERKEMLAA
LIGEGRGHLR YSDHIVGRGE ELFKSFCGAG LEGVISKRVD ARYSGSRSGS WVKTKCIRRQ
EFVILGWTPS DKQRGFRSLL LGVNEKGKLR FAGKVGTGFT GDEIERLMDL MAPLEQKTAT
VEAPRAAVRG AHWIKPKLVA EVAYIEFTDE GVLRHSSYLG LREDKKPEAV VLEIEAPVAT
TANPAATSGV KISNRDRMIF PEGKLTKGEL ADYYEAVAQI MLPWAGSRPI SLVRCPQGRD
KKCFFQKHDA GSFGDDVKQV GILEKDGHQE PYLFVDTPAG LLTCVQMGTI EFHGWGARIE
DVEKADRLVF DLDPDEGLDF KDVVSAAFHL QDVLGQMGLV TFPMVTGGKG VHVIAPLTPT
AEWPQVKDFA HRFAMALAQA DPQRFTAALA KAKRTGKIFI DYLRNQRGAT AVMPYSARSR
PFAPIAVPLT WEELRDLDTP NHWHIGDAPE MLKRAASKNL AHWGRTDQIL PDL
//
