ID   Q2IYX6_RHOP2            Unreviewed;       914 AA.
AC   Q2IYX6;
DT   07-MAR-2006, integrated into UniProtKB/TrEMBL.
DT   07-MAR-2006, sequence version 1.
DT   27-MAR-2024, entry version 97.
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=RPB_1876 {ECO:0000313|EMBL:ABD06584.1};
OS   Rhodopseudomonas palustris (strain HaA2).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Nitrobacteraceae; Rhodopseudomonas.
OX   NCBI_TaxID=316058 {ECO:0000313|EMBL:ABD06584.1, ECO:0000313|Proteomes:UP000008809};
RN   [1] {ECO:0000313|EMBL:ABD06584.1, ECO:0000313|Proteomes:UP000008809}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=HaA2 {ECO:0000313|EMBL:ABD06584.1,
RC   ECO:0000313|Proteomes:UP000008809};
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA   Vergez L., Schmutz J., Larimer F., Land M., Hauser L., Pelletier D.A.,
RA   Kyrpides N., Anderson I., Oda Y., Harwood C.S., Richardson P.;
RT   "Complete sequence of Rhodopseudomonas palustris HaA2.";
RL   Submitted (JAN-2006) to the EMBL/GenBank/DDBJ databases.
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; CP000250; ABD06584.1; -; Genomic_DNA.
DR   RefSeq; WP_011440772.1; NC_007778.1.
DR   AlphaFoldDB; Q2IYX6; -.
DR   STRING; 316058.RPB_1876; -.
DR   KEGG; rpb:RPB_1876; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_1_5; -.
DR   OrthoDB; 9802472at2; -.
DR   Proteomes; UP000008809; 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:ABD06584.1};
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          375..461
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   REGION          223..265
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   914 AA;  100253 MW;  B25DC9C80FE85235 CRC64;
     MAASKTLTLY RNKRDFEQTA EPRGDAEVVP SKRRRFVIQK HDATRLHYDL RLEYDGVFKS
     WAVTRGPSLD PRDKRLAVEV EDHPLDYGDF EGTIPKGQYG GGTVQLWDRG YWDCDDPERG
     FKTGDLKFTL DGEKVHGSWV LVRMRHDRNG GKRTNWLLIK HRDDDAREGK ANDILDEDRS
     VASGRTMKQI AEGKGRAPKP FMTGKVARVK ADAVWDSNKG LAADARAADD AGKAARPKRA
     AAKKAPKKAA AKSRTTKTTS RATRKPVKVA AMPDFIPPQL CTSVERPPGS DGWRHEIKFD
     GYRMQLRIAH GEAALRTRKG LDWTAKFRAI ADEAAGLPDA IIDTEIVALD HHGHPDFAAL
     QAALSDGDSD KLICFAFDLL YADGEDLRSL PLSERKQRLQ DLLKAARGRR KEGLIRYVEH
     FETGGDAILQ SACKLSLEGI VSKKLDAPYR SGRSDNWTKA KCRAGHEVVI GGWKTTAGKF
     RSLMVGVQSD DRAGNHHLAY VGLVGTGFGQ DVVKRILPEL KARASKDNPF AGENAPRKTS
     DVNWVTPDLV AEIEFAGFTG AGMVRQAAFK GLRADKPADE VVAEKPAQVG IARPKPKRGT
     KAAPAVRKVA SAASRAEVMG ISISKPDKVL WPASEISEAI TKLDLAHYYE AVGDWLIAHI
     KGRPCSIVRA PDGIDGEHFF QRHAMPGMSN LIDLAKVSGD RKPYVQIDRV EGLIAVAQIG
     GLELHPWNCA PGAYDVPGRL VFDLDPAPDV GFDDVVAAAR EMKDRLETIG LSTFCKTTGG
     KGLHVVVPLQ PKDDVDWKQA KIFAQTVCAQ MADDSPERYL LNMSKQQRKG KIFLDYLRND
     RMSTAVAALS PRAREGATVS MPVTWSQVKA GLDPKRFTLG TVPALLRKTK AWADYDESAA
     PLRAALEALA SSGA
//