ID   Q92M95_RHIME            Unreviewed;       865 AA.
AC   Q92M95;
DT   01-DEC-2001, integrated into UniProtKB/TrEMBL.
DT   01-DEC-2001, sequence version 1.
DT   27-MAR-2024, entry version 122.
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=SMc03959 {ECO:0000313|EMBL:CAC47322.1};
OS   Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
OS   meliloti).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX   NCBI_TaxID=266834 {ECO:0000313|EMBL:CAC47322.1, ECO:0000313|Proteomes:UP000001976};
RN   [1] {ECO:0000313|EMBL:CAC47322.1, ECO:0000313|Proteomes:UP000001976}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=1021 {ECO:0000313|EMBL:CAC47322.1,
RC   ECO:0000313|Proteomes:UP000001976};
RX   PubMed=11481430; DOI=10.1073/pnas.161294398;
RA   Capela D., Barloy-Hubler F., Gouzy J., Bothe G., Ampe F., Batut J.,
RA   Boistard P., Becker A., Boutry M., Cadieu E., Dreano S., Gloux S.,
RA   Godrie T., Goffeau A., Kahn D., Kiss E., Lelaure V., Masuy D., Pohl T.,
RA   Portetelle D., Puehler A., Purnelle B., Ramsperger U., Renard C.,
RA   Thebault P., Vandenbol M., Weidner S., Galibert F.;
RT   "Analysis of the chromosome sequence of the legume symbiont Sinorhizobium
RT   meliloti strain 1021.";
RL   Proc. Natl. Acad. Sci. U.S.A. 98:9877-9882(2001).
RN   [2] {ECO:0000313|Proteomes:UP000001976}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=1021 {ECO:0000313|Proteomes:UP000001976};
RX   PubMed=11474104; DOI=10.1126/science.1060966;
RA   Galibert F., Finan T.M., Long S.R., Puehler A., Abola P., Ampe F.,
RA   Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G.,
RA   Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P.,
RA   Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F., Gloux S.,
RA   Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M., Hernandez-Lucas I.,
RA   Hong A., Huizar L., Hyman R.W., Jones T., Kahn D., Kahn M.L., Kalman S.,
RA   Keating D.H., Kiss E., Komp C., Lelaure V., Masuy D., Palm C., Peck M.C.,
RA   Pohl T.M., Portetelle D., Purnelle B., Ramsperger U., Surzycki R.,
RA   Thebault P., Vandenbol M., Vorhoelter F.J., Weidner S., Wells D.H.,
RA   Wong K., Yeh K.-C., Batut J.;
RT   "The composite genome of the legume symbiont Sinorhizobium meliloti.";
RL   Science 293:668-672(2001).
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; AL591688; CAC47322.1; -; Genomic_DNA.
DR   RefSeq; NP_386849.1; NC_003047.1.
DR   RefSeq; WP_010970164.1; NC_003047.1.
DR   AlphaFoldDB; Q92M95; -.
DR   EnsemblBacteria; CAC47322; CAC47322; SMc03959.
DR   GeneID; 61604205; -.
DR   KEGG; sme:SMc03959; -.
DR   PATRIC; fig|266834.11.peg.4252; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_2_5; -.
DR   OrthoDB; 9802472at2; -.
DR   Proteomes; UP000001976; 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:CAC47322.1};
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:UP000001976};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          329..453
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   REGION          1..29
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          541..571
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        8..29
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        541..559
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   865 AA;  95261 MW;  A1F873AAB0EEAE40 CRC64;
     MAARNEPLSE YNRRRDFTRT SEPKGAVARR SGDNRMRFLV QKHAATRLHY DFRLEWEGVL
     KSWAVTRGPS LNPEDKRLAV RTEDHPLAYG DFEGTIPKGE YGGGTVMLWD TGWWEPEDDP
     SKALKKGKLS FKLHGSRMKG GWALVRMRPR EGEKRENWLL VKETDDVASD DGESLINENI
     TSIVTGRTME EIAEGRGEKR ARVWHSNKSI SANLKAGAIA ENGNAGKRAT RKASGKLPAF
     KAPQLATLVT KVPAGDAWLN EAKFDGYRLV CAVGAGTVRC YTRNGLDWTE KFPAIAAALA
     ELDCQSALID GEVVALSEGG STFSALQKAL RTGASTRLYA FDLIELDGKD LSRKPLVERK
     ERLEALLQTL GATSTVQFSE HVRGNGEHVL SAICKAGQEG IIAKEADAPY RSGRSRSWLK
     VKCTKRQEFV IGGYTPSSKK GRAFASLLVG TFEGGKLIYR GGVGTGFSGK TMEDLAAAFA
     KRKRDTSPFD SVPRERMRNS VWLEPDLVAE VDFAEFTADG HVRHGSFEGL REDKEARAVK
     LETPKPAEAE PETAKSKSSA RTRKTPPVQG DADVLGIRIS HPDRVLFEGQ GITKIDLARY
     YAVVAERMLP FAADHPVSLV RCPQGGERHC FFQKHASDGF PEAIREVPIT ESSGDTENYM
     YIHDAKGLVA AVQMGTLEFH IWGSSIDRLE KPDRLVFDLD PDPSVDFETV KAAALRLRDE
     LAEIGLKTVP MVTGGKGVHV IVPLRPHAEW EEAKGFAKAL ARSIAERDPD NFVATMSKAK
     RKGKIFIDWL RNDRGATAIA PYSTRARSGG PVATPVGWDE LQGLEAANGF QIPDIIERIE
     AGTDPWREIG KISQSLTKKI LNSVE
//