ID   I3X2Z1_SINF2            Unreviewed;       850 AA.
AC   I3X2Z1;
DT   05-SEP-2012, integrated into UniProtKB/TrEMBL.
DT   05-SEP-2012, sequence version 1.
DT   27-MAR-2024, entry version 66.
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=ykoU2 {ECO:0000313|EMBL:AFL50247.1};
GN   ORFNames=USDA257_c16580 {ECO:0000313|EMBL:AFL50247.1};
OS   Sinorhizobium fredii (strain USDA 257).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX   NCBI_TaxID=1185652 {ECO:0000313|EMBL:AFL50247.1, ECO:0000313|Proteomes:UP000006180};
RN   [1] {ECO:0000313|EMBL:AFL50247.1, ECO:0000313|Proteomes:UP000006180}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=USDA 257 {ECO:0000313|EMBL:AFL50247.1,
RC   ECO:0000313|Proteomes:UP000006180};
RX   PubMed=22843606; DOI=10.1128/JB.00966-12;
RA   Schuldes J., Rodriguez Orbegoso M., Schmeisser C., Krishnan H.B.,
RA   Daniel R., Streit W.R.;
RT   "Complete genome sequence of the broad-host-range strain Sinorhizobium
RT   fredii USDA257.";
RL   J. Bacteriol. 194:4483-4483(2012).
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};
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; CP003563; AFL50247.1; -; Genomic_DNA.
DR   RefSeq; WP_014762428.1; NC_018000.1.
DR   AlphaFoldDB; I3X2Z1; -.
DR   STRING; 1185652.USDA257_c16580; -.
DR   KEGG; sfd:USDA257_c16580; -.
DR   PATRIC; fig|1185652.3.peg.1722; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_0_5; -.
DR   Proteomes; UP000006180; 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:AFL50247.1};
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   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          332..472
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          186..218
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..24
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   850 AA;  94080 MW;  172827A3D2947FE4 CRC64;
     MGLDLYREKR DFDSTPEPKG RKARRAGNSF VVQKHDATRL HYDFRLEMDG VLKSWAVTKG
     PSLIPGEKRL AVHVEDHPLE YGDFEGTIPK GEYGGGTVIL WDRGTWSPIG DARRGYAKGH
     LDFELSGEKL GGRWHLVRMA GKPREKRENW LLIKGDDQAA RSEEDPDILE ERPESVLTGR
     EIKDVAGEEP GWSSKTGRIR KRARSKKTTA PQEQEPEAVM NVPDPSKIKG AKAAALPDFV
     EPSLATLVSS APAGERWLHE IKFDGYRLQA RIEAGRVRLL TRSGLDWTKR FGKALVSALQ
     ALPVGTALID GEIVVETGSG ASDFSGLQAD LSEGRSDRFR FYVFDLLYLD GYDLRALPLI
     KRKELLDQLI GEDDGIVRFS SHFEEEGRLV LSHACRLSLE GIVSKLRDAP YRTGRNKSWV
     KSKCSARQEF VVAGYVPSTT SRKAIGSLVL GVYDGDKLDH VGRVGTGFTA ALAEDLLKRL
     DRLRTSESPF AARLSAEDAR QVRYVKPELV AEVEFRAWTA DGHLRHASFR GLREDRLAGE
     IVRETPKSTG TQPKPPRRTV KLTHPDRLYW PDEGVTKEGL ADYYAEVWRF IGPHIVGRPL
     ALVRCPNGIT GEQFFQKHAW KGLNPNIVLV NDPKEPPDEQ LLSIRDLDGL IALVQSAVLE
     IHPWGSTVAD WEKPDTIIMD LDPGEDVPFE AVIDAAFETA DRLKAAGLVP FVKTSGGKGL
     HVVAPLIPKA EWPAVKAFTK SIADAMASDS SDRFVSTITK SKRRGKILVD YLRNQRGATA
     VAAYSTRARP GAAVSMPLSW DELAPGIGPA YFTVENTPTR LQSLSADPWA DFRAAAIPLK
     EPKAGRRKAA
//