ID A0A0U3LYM1_9BURK Unreviewed; 861 AA.
AC A0A0U3LYM1;
DT 16-MAR-2016, integrated into UniProtKB/TrEMBL.
DT 16-MAR-2016, sequence version 1.
DT 24-JAN-2024, entry version 31.
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=Hrubri_2562 {ECO:0000313|EMBL:ALU89743.1};
OS Herbaspirillum rubrisubalbicans M1.
OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC Oxalobacteraceae; Herbaspirillum.
OX NCBI_TaxID=1078773 {ECO:0000313|EMBL:ALU89743.1, ECO:0000313|Proteomes:UP000069903};
RN [1] {ECO:0000313|EMBL:ALU89743.1, ECO:0000313|Proteomes:UP000069903}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=M1 {ECO:0000313|EMBL:ALU89743.1,
RC ECO:0000313|Proteomes:UP000069903};
RA Balsanelli E., Cardoso R.L.A., Cruz L.M., Faoro H., Chubatsu L.S.,
RA Muller-Santos M., Baura V.A., Huergo L.F., Wassem R., Broughton W.,
RA Monteiro R.A., Souza E.M., Pedrosa F.O.;
RT "Herbaspirillum rubrisubalbicans M1 complete genome.";
RL Submitted (DEC-2015) 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; CP013737; ALU89743.1; -; Genomic_DNA.
DR RefSeq; WP_058895708.1; NZ_CP013737.1.
DR AlphaFoldDB; A0A0U3LYM1; -.
DR STRING; 1078773.Hrubri_2562; -.
DR KEGG; hrb:Hrubri_2562; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000069903; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:InterPro.
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:0006310; P:DNA recombination; IEA:InterPro.
DR GO; GO:0006281; P:DNA repair; IEA:InterPro.
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; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING 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:ALU89743.1};
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 313..420
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 1..32
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 519..561
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 544..558
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 861 AA; 95160 MW; BADE89C8697B24B2 CRC64;
MSASSLDRYH ARRDFSITPE PSGHGRQTAR SAQGPLQFFI QRHHARRLHY DFRLELDGVL
KSWAVPKGPS LDPHDKRLAV RVEDHPLDYG SFEGDIPAQQ YGAGHVVLWD RGQWLPHGDP
QAGLKQGHLG FTLQGDKLQG RWALVRMGKP ERDGKENWLL IKEDDAAAQT GEAAAITELR
PESVKDRGDL PSAASELAHG VSQADAIEPH PARIPDVMPA QLATLVDQAP QGEDWLCELK
FDGYRGLCRI EGGQAAIYTR EGLDWSHRWP VLVQALARLP VDQAWIDGEV VALDAAGHIS
FEALQNLVRG DRQQADGIRL ALYVFDLPYL NGYDLRAVPL TQRKALLREL VPGSDEEGLL
LYSEHLLGHA DEVLRHACQH GMEGIVVKRA DAPYSGRRDR NWLKLKCEQR QEFVIAGYTD
PAGQRSGFGA ILVGVYDDQG QLHYAGRVGT GFDERLLGRM LKLFQRLEQD RPAFVDPPTG
QQRRGVHWLK PELVAEVKFA QWTKSGILRH GSFVALREDK PPTSIVRETQ QPVAADAPAA
EEGTAPSPPS PPSRRPSPAD LSQPVMVAGV KLTHPGKILF PATGLTKLEL ARYYQSVAPW
ILPELKQRPL SLVRCPDGQA GKCFFQKHSG QGMPEAIDTI QVPEGEGTAQ YMMVNDVAGL
VATVQMGVLE LHAWGATGRA LDQPDRVVFD LDPAPDVPWA SVVEGAQLVR ALLQEIGLES
YLKTSGGKGL HVMVPMRPEH DWDVVKDWAH RLAAHLARLL PERFIARMSK AARAGKIFID
YLRNAPGATT VVAYSVRARD GAPVSVPITW EELEQGVRAD HFKVATMPQR LQSLAHSDPW
AGFGQPRQRL TKAMLAAFDP V
//