ID   B9K4A7_ALLAM            Unreviewed;       893 AA.
AC   B9K4A7;
DT   24-MAR-2009, integrated into UniProtKB/TrEMBL.
DT   24-MAR-2009, sequence version 1.
DT   27-MAR-2024, entry version 85.
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:ACM39557.1};
GN   OrderedLocusNames=Avi_8017 {ECO:0000313|EMBL:ACM39557.1};
OS   Allorhizobium ampelinum (strain ATCC BAA-846 / DSM 112012 / S4)
OS   (Agrobacterium vitis (strain S4)).
OG   Plasmid pTiS4 {ECO:0000313|EMBL:ACM39557.1,
OG   ECO:0000313|Proteomes:UP000001596}.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Rhizobiaceae; Rhizobium/Agrobacterium group; Allorhizobium;
OC   Allorhizobium ampelinum.
OX   NCBI_TaxID=311402 {ECO:0000313|EMBL:ACM39557.1, ECO:0000313|Proteomes:UP000001596};
RN   [1] {ECO:0000313|EMBL:ACM39557.1, ECO:0000313|Proteomes:UP000001596}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=S4 / ATCC BAA-846 {ECO:0000313|Proteomes:UP000001596};
RC   PLASMID=pTiS4 {ECO:0000313|EMBL:ACM39557.1,
RC   ECO:0000313|Proteomes:UP000001596};
RX   PubMed=19251847; DOI=10.1128/JB.01779-08;
RA   Slater S.C., Goldman B.S., Goodner B., Setubal J.C., Farrand S.K.,
RA   Nester E.W., Burr T.J., Banta L., Dickerman A.W., Paulsen I., Otten L.,
RA   Suen G., Welch R., Almeida N.F., Arnold F., Burton O.T., Du Z., Ewing A.,
RA   Godsy E., Heisel S., Houmiel K.L., Jhaveri J., Lu J., Miller N.M.,
RA   Norton S., Chen Q., Phoolcharoen W., Ohlin V., Ondrusek D., Pride N.,
RA   Stricklin S.L., Sun J., Wheeler C., Wilson L., Zhu H., Wood D.W.;
RT   "Genome sequences of three Agrobacterium biovars help elucidate the
RT   evolution of multichromosome genomes in bacteria.";
RL   J. Bacteriol. 191:2501-2511(2009).
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; CP000637; ACM39557.1; -; Genomic_DNA.
DR   RefSeq; WP_012648924.1; NC_011982.1.
DR   AlphaFoldDB; B9K4A7; -.
DR   KEGG; avi:Avi_8017; -.
DR   HOGENOM; CLU_008325_0_1_5; -.
DR   Proteomes; UP000001596; Plasmid pTiS4.
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:ACM39557.1};
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:ACM39557.1};
KW   Reference proteome {ECO:0000313|Proteomes:UP000001596};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          344..481
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          225..254
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          546..586
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..20
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        546..569
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   893 AA;  98374 MW;  25FBFD8BB5F51957 CRC64;
     MPDNLSKYRE KRDFKKTAEP SGEVGVKSSN RRRFVIQKHD ATRLHYDLRI EMDGVFKSWA
     VTKGPSLDPH DKRLAVEVED HPLDYGDFEG TIPKGQYGGG TVMLWDRGYW EPEGNKTAEQ
     ALAKGDFKFT LEGERLHGSF VLVRMRGREG EKRTNWLLIK HHDDHAVEEN GAAILEENDT
     SVASGRTMEA IASGKGRKPK PFMTQGSVVE ADAVWDSTEG LAADERKAGT KTKAKPTKKA
     AAAAKQPNTG MPEFVPPQLC ETFSRPPSAE GWIHEVKFDG YRIQMRVVDG NVTLKTRKGL
     DWTAKWPAIA KAASSLPDCI IDGEICALDN HGAPDFAALQ AALSEEKTDD LVFFGFDLLF
     EGEEDLREAP LTERKERLSA MLSDAGDDPR LRFVEHFETG GDAVLKSACR LSLEGIVSKK
     GDAPYQSGRS DTWTKSKCRA GHEVVIGAYA TTNGAFRSLL VGVYRGDHFV YVGRVGTGYG
     AKVVDQILPK LQALEASKSP FTGIGAPKKA AEIVWLKPEL VAEIEFAGWT ADGQVRQAAF
     KGLREDKPAK EVEAEKPAEP AEVDTPDPET ARKPAPTPTT SSRLRKGAKV DVMGVLVSSP
     DKELWPDALD GEPVTKVDLA HYYEAVGPWL IDHIKGRPCS IIRTPDGIGG EQFFQRHAMQ
     GTSNLIEQVK VSGDKQPYLQ IGRVEGLAAI AQIGGAELHP WNCEPYQPEV PGRLVFDLDP
     GPDVDFATVV EGAREIRDRL EELGLVSFCK TTGGKGLHVV TPLAVPKGKK LSWDEGKAFA
     HDVCLQMARD NPELYLTKMS KAQREGRIFL DYLRNDRTST AVAPLSPRAR PGATVSMPLN
     WAQVKKGLDP KRFTIRTVPG LLKDNTAWQD YCDGQRPLEQ AIKRLEKLMR RAA
//