ID   Q2K0P3_RHIEC            Unreviewed;       882 AA.
AC   Q2K0P3;
DT   07-MAR-2006, integrated into UniProtKB/TrEMBL.
DT   07-MAR-2006, sequence version 1.
DT   27-MAR-2024, entry version 112.
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=RHE_PE00252 {ECO:0000313|EMBL:ABC93687.1};
OS   Rhizobium etli (strain CFN 42 / ATCC 51251).
OG   Plasmid p42e {ECO:0000313|EMBL:ABC93687.1,
OG   ECO:0000313|Proteomes:UP000001936}.
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
OX   NCBI_TaxID=347834 {ECO:0000313|EMBL:ABC93687.1, ECO:0000313|Proteomes:UP000001936};
RN   [1] {ECO:0000313|EMBL:ABC93687.1, ECO:0000313|Proteomes:UP000001936}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=CFN 42 / ATCC 51251 {ECO:0000313|Proteomes:UP000001936};
RX   PubMed=16505379; DOI=10.1073/pnas.0508502103;
RA   Gonzalez V., Santamaria R.I., Bustos P., Hernandez-Gonzalez I.,
RA   Medrano-Soto A., Moreno-Hagelsieb G., Janga S.C., Ramirez M.A.,
RA   Jimenez-Jacinto V., Collado-Vides J., Davila G.;
RT   "The partitioned Rhizobium etli genome: genetic and metabolic redundancy in
RT   seven interacting replicons.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:3834-3839(2006).
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; CP000137; ABC93687.1; -; Genomic_DNA.
DR   RefSeq; WP_011428106.1; NC_007765.1.
DR   AlphaFoldDB; Q2K0P3; -.
DR   KEGG; ret:RHE_PE00252; -.
DR   HOGENOM; CLU_008325_0_1_5; -.
DR   OrthoDB; 9802472at2; -.
DR   Proteomes; UP000001936; Plasmid p42e.
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:ABC93687.1};
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:ABC93687.1};
KW   Reference proteome {ECO:0000313|Proteomes:UP000001936};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          339..432
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   COMPBIAS        7..32
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   882 AA;  97521 MW;  8C9E45DB21C6FFE6 CRC64;
     MASDKLSSYR SKRDFQKTAE PSGERSLKQS NRRRFVIQKH DATRLHYDLR LELDGVFKSW
     AVTKGPSLDP HDKRLAVEVE DHPLDYGDFE GTIPKGQYGG GTVMLWDRGY WEPEGRKSPE
     QALSKGDFKF TLEGERLHGS FVLVRMRNDR ERSKRTNWLL IKHHDEFSVD ENGASILEEN
     VTSVASGRSM EMIAAGKGRK PKPFMVEGGK VQADAVWDSN HGLAAEERQS EASAGKRAGT
     ATAVDLPDFI APQLCEKVER PPGGDGWIHE IKFDGYRIQM RVLDGEVTLK TRKGLDWTAK
     YPEIAEAASG LPDCILDGEI CALDEQGAPN FAALQAALSE GKTASLVYFA FDLLYDGGED
     LRSKPLIERK RRLQELLTEA GNDPRIRYVE HFETGGDAVL RSACKLSLEG IISKQTDAPY
     QSGRTESWAK SKCRAGHEVV IGAYAKTNGR FRSLLAGVFR GDHFVYVGRV GTGYGAKKVE
     TLLPKLKALE TARSPFTGIG APKKQAEVVW VKPELVAEIE FEGWTADGLV RQAAFKGLRE
     DKPAREVEAE PPVRPAKADI AEPVPRARQT PARRKGAKAD VMGVLISNPD KPLWPDANGS
     EPVTKEELAG YYEAVGDWMI DHIKGRPCSI IRAPDGIGGE QFFQRHAMPG QSNLLDLVKV
     FGDKKPYLQI DRIEGLAAVA QIAAVELHPW NCEPGQPEVP GRLVFDLDPG PDVPFATVVA
     AAREMRDRLE DLGLISFCKT TGGKGLHVVT PLAVNKRKPL SWPEAKAFAH DVCQQMARNN
     PDLYLIKMTK SLRGGRIFLD YLRNDRMATA VAPLSPRARP GATVSMPLTW TQVKSDLDPK
     RFTIRTVPAL LSKSSAWKDY CEGQRPLEQA IKKLGRAGKH AA
//