ID   Q98P39_RHILO            Unreviewed;       883 AA.
AC   Q98P39;
DT   01-OCT-2001, integrated into UniProtKB/TrEMBL.
DT   01-OCT-2001, sequence version 1.
DT   27-MAR-2024, entry version 118.
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=mll9625 {ECO:0000313|EMBL:BAB54816.1};
OS   Mesorhizobium japonicum (strain LMG 29417 / CECT 9101 / MAFF 303099)
OS   (Mesorhizobium loti (strain MAFF 303099)).
OG   Plasmid pMLb {ECO:0000313|EMBL:BAB54816.1,
OG   ECO:0000313|Proteomes:UP000000552}.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Phyllobacteriaceae; Mesorhizobium.
OX   NCBI_TaxID=266835 {ECO:0000313|EMBL:BAB54816.1, ECO:0000313|Proteomes:UP000000552};
RN   [1] {ECO:0000313|EMBL:BAB54816.1, ECO:0000313|Proteomes:UP000000552}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LMG 29417 / CECT 9101 / MAFF 303099
RC   {ECO:0000313|Proteomes:UP000000552};
RC   PLASMID=pMLb {ECO:0000313|EMBL:BAB54816.1,
RC   ECO:0000313|Proteomes:UP000000552};
RX   PubMed=11214968; DOI=10.1093/dnares/7.6.331;
RA   Kaneko T., Nakamura Y., Sato S., Asamizu E., Kato T., Sasamoto S.,
RA   Watanabe A., Idesawa K., Ishikawa A., Kawashima K., Kimura T., Kishida Y.,
RA   Kiyokawa C., Kohara M., Matsumoto M., Matsuno A., Mochizuki Y.,
RA   Nakayama S., Nakazaki N., Shimpo S., Sugimoto M., Takeuchi C., Yamada M.,
RA   Tabata S.;
RT   "Complete genome structure of the nitrogen-fixing symbiotic bacterium
RT   Mesorhizobium loti.";
RL   DNA Res. 7:331-338(2000).
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; AP003017; BAB54816.1; -; Genomic_DNA.
DR   RefSeq; WP_010916160.1; NC_002682.1.
DR   AlphaFoldDB; Q98P39; -.
DR   KEGG; mlo:mll9625; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_1_5; -.
DR   Proteomes; UP000000552; Plasmid pMLb.
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:BAB54816.1};
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:BAB54816.1};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          340..477
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          542..578
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        542..559
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   883 AA;  97530 MW;  EB0DB180BF8A9CDC CRC64;
     MASDKLTTYK AKRDFKKTQE PSGQGSVKPS NRRRFVIQKH DATRLHYDLR LELGGVFKSW
     AVTRGPSLDP HDKRLAVEVE DHPLDYGDFE GTIPKGQYGG GTVMLWDRGY WEPEGKNSPE
     QALAKGDFKF TLEGERLHGS FVLVRMANDR ERGKRTNWLL IKHRDEYAVE TNGAAILDKN
     DTSVASGRKM EAIAAGKGRS PKPFMLQGGK AEADAVWDSR TGLAAQERKT NIRAKRKKHG
     TVTAADLPDF IAPQLCQTLA RPPSESGWLH EIKFDGYRIQ MRVLGGEAIL QTRKGLDWTA
     RYRAIARAAG NLPDAIIDGE ICALDENGAP DFAALQAALA EGKTDALVYF AFDLLFEGAE
     DLRVLPLSKR KARLRQFLTD TGEDDRIRFV EHFETGGEAV LRSACRLSLE GIVSKRADAP
     YVSGRTETWA KSKCRAGHEV VIGAYATTNG KFRSLLVGVY RGDHFVYVGR VGTGYGAAKV
     RDLLPKLKAA ATRKSPFTGI GAPKNEPGVV WLKPELVAEI EFAGWTSDGL VRQAAFKGLR
     EDKPAEEVEA DKPASPEKTK VPQPREPTAA AKPSRSRGKV DVMGVLISNP DKPLWPDAND
     GIPVTKEDLA RYYEAVGPWL IEHIRGRPCS IIRAPDGFGG EQFFQRHAMP GTSNLLELVE
     VFGDKKPYLQ IDRVEGLAAV AQIGALELHP WNCEPQQPEV PGRLVFDLDP GPDVPFKTVV
     EAAKEMRARL DDLGLVSFCK TTGGKGLHVV TPLAVTKRSK LTWPEAKGFA HDVCLQMARD
     NPALYLTKMA KNQRIGRIFL DYLRNDRMAT AVAPLSPRAR PGATVSMPLT WAQVKTDLDP
     KRFTLRTVPG LLAKSTAWKD YGDGHRLLEA SIKRLARSMR RAA
//