ID Q6N3P3_RHOPA Unreviewed; 914 AA.
AC Q6N3P3;
DT 05-JUL-2004, integrated into UniProtKB/TrEMBL.
DT 05-JUL-2004, sequence version 1.
DT 24-JAN-2024, entry version 110.
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 OMA; YMANLGC; -.
DR PhylomeDB; Q6N3P3; -.
DR Proteomes; UP000001426; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:InterPro.
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:0006310; P:DNA recombination; IEA:InterPro.
DR GO; GO:0006281; P:DNA repair; IEA:InterPro.
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; BIFUNCTIONAL NON-HOMOLOGOUS END JOINING 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
//