ID   A4Z011_BRASO            Unreviewed;       904 AA.
AC   A4Z011;
DT   29-MAY-2007, integrated into UniProtKB/TrEMBL.
DT   29-MAY-2007, sequence version 1.
DT   27-MAR-2024, entry version 87.
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   OrderedLocusNames=BRADO5823 {ECO:0000313|EMBL:CAL79487.1};
OS   Bradyrhizobium sp. (strain ORS 278).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Nitrobacteraceae; Bradyrhizobium.
OX   NCBI_TaxID=114615 {ECO:0000313|EMBL:CAL79487.1, ECO:0000313|Proteomes:UP000001994};
RN   [1] {ECO:0000313|EMBL:CAL79487.1, ECO:0000313|Proteomes:UP000001994}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ORS 278 {ECO:0000313|Proteomes:UP000001994};
RX   PubMed=17540897; DOI=10.1126/science.1139548;
RA   Giraud E., Moulin L., Vallenet D., Barbe V., Cytryn E., Avarre J.C.,
RA   Jaubert M., Simon D., Cartieaux F., Prin Y., Bena G., Hannibal L.,
RA   Fardoux J., Kojadinovic M., Vuillet L., Lajus A., Cruveiller S., Rouy Z.,
RA   Mangenot S., Segurens B., Dossat C., Franck W.L., Chang W.S., Saunders E.,
RA   Bruce D., Richardson P., Normand P., Dreyfus B., Pignol D., Stacey G.,
RA   Emerich D., Vermeglio A., Medigue C., Sadowsky M.;
RT   "Legumes symbioses: absence of nod genes in photosynthetic bradyrhizobia.";
RL   Science 316:1307-1312(2007).
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; CU234118; CAL79487.1; -; Genomic_DNA.
DR   RefSeq; WP_012029390.1; NC_009445.1.
DR   AlphaFoldDB; A4Z011; -.
DR   STRING; 114615.BRADO5823; -.
DR   KEGG; bra:BRADO5823; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_1_5; -.
DR   OrthoDB; 9802472at2; -.
DR   Proteomes; UP000001994; 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:CAL79487.1};
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:UP000001994};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          355..450
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   REGION          216..261
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   904 AA;  99183 MW;  AD28102C5609AF33 CRC64;
     MALKKLSTYR KKRDFEKTAE PSGDARIAPA ARPRFVIQKH DATRLHYDLR LEFDGVFKSW
     AVTKGPSLDP HDKRLAVEVE DHPLDYGDFE GTIPEGEYGG GTVMLWDRGY WESDDPERGF
     TKGDLKFTLE GEKLHGSWVL VRMRHDRTGG KRTNWLLIKH RDEFAREGAA NDVLDADKSV
     ASGRTMEQIA AGKGRAPKPF MLAKRQRMNA DAIWHSNRSD GETKTSKVST KAASSRTKAA
     KAGRAKSSRV SKMAEPKTVS SLPDFVPPEL CTSVAQPPSG EGWAHEIKFD GYRVQIRVED
     GQAALKTRKG LDWTAKFGVI AEAAAKLPDA IIDGEIVALD KDGNPNFSAL QAAISAGQTD
     ELVFFAFDLM FVEEFDLRRQ PLRERKARLA KLLKANIKGK TPVIRYVEHF ESDGEAVLES
     ARKLSLEGIV SKKLDSAYHS GRTESWTKAK TRPGHEVVVG GWKTTNGKFR SLMVGVNKDD
     HLAYVGIVGT GFGQDTVKAI MPALKAAASD KSPFSGKNAP RKAREVHWLK PELVAEIEFA
     GFTGDGNVRQ ASFKGLRQDK PAREVVAEEP VVAAKVTKPV ARAAATVATG GTTVHKTPSR
     TKGAATVMGV AISKPDKALW PDAGDGEPVT KLDLATYLEA VGDWMIEHLK GRPCSIVRAP
     DGIGGERFFQ RHGMQGMSDL LELVKVSGDR KPYLQIDRVE GLIAVAQVAA VELHPWNCAP
     DAYDVPGRLV FDLDPAPNVA FEEVIAAAKE MRQRLKTLGL ESFCKTTGGK GLHVVTPLLH
     GARDQVTWPE AKAFAQGVCQ WMANDSPDDY LLNMSKKLRK GKIFLDYLRN DRMSTAVAVL
     SPRAREGATV SMPVTWAQVK NGLDPKRYTI RTVPALLAKT KAWDGYDDAA GAIRPAIRKL
     TDTL
//