ID   Q13Z47_PARXL            Unreviewed;      1001 AA.
AC   Q13Z47;
DT   22-AUG-2006, integrated into UniProtKB/TrEMBL.
DT   22-AUG-2006, sequence version 1.
DT   27-MAR-2024, entry version 101.
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=Bxe_A2328 {ECO:0000313|EMBL:ABE30642.1};
OS   Paraburkholderia xenovorans (strain LB400).
OC   Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales;
OC   Burkholderiaceae; Paraburkholderia.
OX   NCBI_TaxID=266265 {ECO:0000313|EMBL:ABE30642.1, ECO:0000313|Proteomes:UP000001817};
RN   [1] {ECO:0000313|EMBL:ABE30642.1, ECO:0000313|Proteomes:UP000001817}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=LB400 {ECO:0000313|EMBL:ABE30642.1,
RC   ECO:0000313|Proteomes:UP000001817};
RX   PubMed=17030797; DOI=10.1073/pnas.0606924103;
RA   Chain P.S., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L.,
RA   Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M., Lao V.,
RA   Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J.,
RA   Parnell J.J., Ramette A., Richardson P., Seeger M., Smith D., Spilker T.,
RA   Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., Tiedje J.M.;
RT   "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome
RT   shaped for versatility.";
RL   Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(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; CP000270; ABE30642.1; -; Genomic_DNA.
DR   RefSeq; WP_011488273.1; NZ_CP008760.1.
DR   AlphaFoldDB; Q13Z47; -.
DR   STRING; 266265.Bxe_A2328; -.
DR   KEGG; bxb:DR64_32; -.
DR   KEGG; bxe:Bxe_A2328; -.
DR   PATRIC; fig|266265.5.peg.2201; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   OrthoDB; 9802472at2; -.
DR   Proteomes; UP000001817; Chromosome 1.
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:ABE30642.1};
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          389..516
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   REGION          1..41
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          208..264
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          603..682
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1..22
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        212..226
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        606..645
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        646..660
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   1001 AA;  108786 MW;  C93F40DDE8EC7F7C CRC64;
     MNDRLDTYNR KRRFDDTPEP AGTRTSRKQG GRKTAGQASP EALSYVIQEH DARRLHYDFR
     LELNGTLLSW AVPKGPSLDP SVKRLAVHVE DHPVEYGSFE GEIPLGNYGA GSVIVWDRGT
     WEPLGGAAEA ARAYAAGKLK FQLHGEKLHG GWTLVRSHMR GSGDKEQWLL IKERDDEARD
     ESKYDILKKR PGSVLADSAA AVKGAKTAKT AAAKSTAKTA SKAAVATATK ATADPDSASL
     AKRTGRNGAQ KASSSRADPK RPDIVATRSA QSLRDLAASP SIEGAVPARL PATFKPQLAT
     LVDGAPPGNE WSYEIKFDGY RVLVRIDRAT KGSAVKVLTR AGNDWTAKFS KQVKAFEQLD
     IESAWLDGEA VVLNQNGVPN FQALQNAFDS NRPQDIVIYL FDIPFLNGYD LRGVPLEQRR
     AILRALLEDA DDSVLRFSNN FEFSADDLLR SACDMALEGI IGKRRDSGYM SGRSSAWIKL
     KCRRRQEFVI GGYSEPSGSR AAFGALLLGV YDGNGKLQYA GRVGTGFDAA LLRSVKKELD
     AHETRHMPFA AAPRERSRTP VHWVEPVLVA ECNFAEWTSD GIVRQASFVS LRSDKPARQI
     VKETPRQGAD VQQQTDSVSN DAPTKRAARK TSASAATTSG EGKTRVAKSK TADAKDASTK
     SRGVEASGAK GSAAKAAATK PTAATAKAAK ATKTSAAKAN TTSAPGEVAG VRVSHPDRVI
     DRSTGTRKID LVRYYESVAD WMLPHLRDRP VSLVRAPEDI DGELFFQKHS QKLSIPNVTQ
     HPGLDPGHPP LITVDTLKAL VGAAQMGTVE FHTWNAVVSN IEKPDRMVFD LDPDASLGWE
     RMIEAAQLTR SLLEELGLAS FCKTSGGKGF HVVVPLAKQA GWDEVKDFSQ AVAQHMAATL
     PRYFSAKMGA QNRKQKIFVD YLRNNRGSST VAAFSARARP GLGVSVPLAW DEVATTTGGA
     QWTIENLHER LADLKSDPWA DYAKTRQRIT AAMKKRLDDA Q
//