ID   Q6N3P3_RHOPA            Unreviewed;       914 AA.
AC   Q6N3P3;
DT   05-JUL-2004, integrated into UniProtKB/TrEMBL.
DT   05-JUL-2004, sequence version 1.
DT   27-MAR-2024, entry version 111.
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=RPA3650 {ECO:0000313|EMBL:CAE29091.1};
OS   Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Nitrobacteraceae; Rhodopseudomonas.
OX   NCBI_TaxID=258594 {ECO:0000313|EMBL:CAE29091.1, ECO:0000313|Proteomes:UP000001426};
RN   [1] {ECO:0000313|EMBL:CAE29091.1, ECO:0000313|Proteomes:UP000001426}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-98 / CGA009 {ECO:0000313|Proteomes:UP000001426};
RX   PubMed=14704707; DOI=10.1038/nbt923;
RA   Larimer F.W., Chain P., Hauser L., Lamerdin J., Malfatti S., Do L.,
RA   Land M.L., Pelletier D.A., Beatty T.J., Lang A.S., Tabita F.R.,
RA   Gibson J.L., Hanson T.E., Torres y Torres J., Peres C., Harrison F.H.,
RA   Gibson J., Harwood C.S.;
RT   "Complete genome sequence of the metabolically versatile photosynthetic
RT   bacterium Rhodopseudomonas palustris.";
RL   Nat. Biotechnol. 22:55-61(2004).
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; BX572604; CAE29091.1; -; Genomic_DNA.
DR   RefSeq; WP_011159189.1; NZ_CP116810.1.
DR   AlphaFoldDB; Q6N3P3; -.
DR   STRING; 258594.RPA3650; -.
DR   GeneID; 66894755; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_1_5; -.
DR   PhylomeDB; Q6N3P3; -.
DR   Proteomes; UP000001426; 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:CAE29091.1};
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:UP000001426};
KW   Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT   DOMAIN          372..458
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          227..272
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        7..29
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   914 AA;  99962 MW;  BC40ABEC6A8BD78A CRC64;
     MASNKLSIYR KKRDFEQTAE PRGDAKVAPS KQRRFVIQKH DATRLHYDLR LEYGGVFKSW
     AVTKGPSLDP NDKRLAVEVE DHPLDYGDFE GTIPKGQYGG GTVQLWDRGY WECDDPERGF
     KTGDLKFTLH GEKLHGSWVL VRMRHDRSGG KRTNWLLIKH RDDDAREGDA NTVLDEDRSV
     ASGRAMDTIA EGKGKAPKPF MLRKAATRVT ADAVWDSNTG LAADKRAETG AAKKVAKSKP
     TTSAKAKAAK SAKPASRSKP AAQGKRAAMP DFVPPQLCTS VERPPGGEGW GHEIKFDGYR
     MQLRVEHGEA RLLTRKGLDW TAKFGAIADE AASLPDAIID TEVVALDSHG QPDFASLQAA
     LSDGHTENLI CFAFDLLYVD GEDLRGLPLA ERKARLAALL KAARGRRKEG LIRYVEHFDT
     GGDAILQSAC KLSLEGIVSK KLDAAYRSGR SDGWTKAKCR AGHEVVIGGW KTTNGKFRSL
     LVGVHRGDDL AYVGIVGTGF GQDVVKRILP ELKAHKADTS PFSGANAPKK TREVHWVTPD
     LVAEIEFAGF TGAGMVRQAS FKGLRADKPA EEVEAEEPQR VELAEPAPMR RIAKASKSGK
     PAAKRAAPRR ADAARSEVMG VAISKPDKEL WPASEIGAAI TKRDLADYFA EVGDWLIPHI
     KGRPCSILRA PDGIDGEHFF QRHAMPGMSN LIGLAKVSGD RKPYVQIDRV EGLIAAAQIG
     GVELHPWNCA PNRYDVPGRL VFDLDPAPEV GFDEVITAAK EMKQRLEALG LKTFCKTTGG
     KGLHVVVPLK PDDGIDWKAA KTFAQTVCAQ MAEDSPEQYL LNMSKRKRIG KIFLDYLRND
     RMSTAVAVLS PRARTGATVS MPLTWSQVKA GLDPKRYTIE SVPALIKRSK AWTDYDDAAT
     PLKAAIRTLT SGKT
//