ID   Q133M6_RHOPS            Unreviewed;       930 AA.
AC   Q133M6;
DT   31-OCT-2006, integrated into UniProtKB/TrEMBL.
DT   31-OCT-2006, sequence version 1.
DT   27-MAR-2024, entry version 91.
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=RPD_3490 {ECO:0000313|EMBL:ABE40713.1};
OS   Rhodopseudomonas palustris (strain BisB5).
OC   Bacteria; Pseudomonadota; Alphaproteobacteria; Hyphomicrobiales;
OC   Nitrobacteraceae; Rhodopseudomonas.
OX   NCBI_TaxID=316057 {ECO:0000313|EMBL:ABE40713.1, ECO:0000313|Proteomes:UP000001818};
RN   [1] {ECO:0000313|EMBL:ABE40713.1, ECO:0000313|Proteomes:UP000001818}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=BisB5 {ECO:0000313|EMBL:ABE40713.1,
RC   ECO:0000313|Proteomes:UP000001818};
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA   Hauser L., Pelletier D.A., Kyrpides N., Lykidis A., Oda Y., Harwood C.S.,
RA   Richardson P.;
RT   "Complete sequence of Rhodopseudomonas palustris BisB5.";
RL   Submitted (MAR-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; CP000283; ABE40713.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q133M6; -.
DR   STRING; 316057.RPD_3490; -.
DR   KEGG; rpd:RPD_3490; -.
DR   eggNOG; COG1793; Bacteria.
DR   eggNOG; COG3285; Bacteria.
DR   HOGENOM; CLU_008325_0_1_5; -.
DR   Proteomes; UP000001818; 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:ABE40713.1};
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          381..467
FT                   /note="ATP-dependent DNA ligase family profile"
FT                   /evidence="ECO:0000259|PROSITE:PS50160"
FT   REGION          227..276
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          578..634
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        257..271
FT                   /note="Basic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        578..596
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        607..625
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ   SEQUENCE   930 AA;  101391 MW;  EA276BD0346EA711 CRC64;
     MVAGKTLTLY RNKRDFEQTA EPRGDGKVAP SKRRRFVIQK HDATRLHYDL RLEYNGVFKS
     WAVTRGPSLD PHDKRLAVEV EDHPLDYGDF EGTIPKGQYG GGTVQLWDRG YWECDDPERG
     FKKGDLKFSL DGEKLQGSWV LVRMRHDRNG GKRTNWLLIK HRDDDAREGK ANDILDQDRS
     VASGRAMTEI AQGKGRAPKP FMTGKAARVK ADAVWNSKEG LAADERAANG AGGAVASKPA
     PPNKAKATTA KSKTAKSKTA KVAKPKPGRK AAAKRAAMPD FVPPQLCTSV ERPPGGDGWG
     HEIKFDGYRM QLRVDAGEAT LKTRKGLDWT ARFQAIADQA AGLPDALIDT EIVALDQHGH
     PDFAALQAAL SDGDTDNLIC FAFDLLHADG EDLRALPLSD RKRRLQELLT AARGRRKQGL
     IRYVEHFDTG GDAILQSACK LSLEGIVSKK LDAPYRSGRS DNWTKAKCRA GHEVVIGGWK
     TNAGKFRSLL VGVHHDDHLA YVGIVGTGFG QDVVKRLLPE LKAHAAKDNP FAGENAPRKT
     ADVHWLAPEL VAEIEFAGFT GAGMVRQAAF KGLRADKPAG EVEAEEPAKV DIAGPKPGRR
     AKPSSNAKSA KPKTATPNAG RSKTRATHAS RAEVMGVVIS KPDKELWPAS RIGDAVNKRD
     LAHYYEAVGD WMIPHLEGRP CSIVRAPDGI GGEHFFQRHA MPGMSNLIAL AKVAGDRKPY
     VQIDRVEGLI AAAQIGGLEL HPWNCAPGRY EVPGRLVFDL DPAPEVGFDA VIVAAREMKD
     RLEAIGLPSF CKTTGGKGLH VVTPLVPSDD IDWKQAKIFA QTVCAGMADD SPDRYLLNMS
     KQQRKGKIFL DYLRNDRMST AVAVLSPRAR EGATVSMPLT WTQVKAGLDP KRYTVETVPA
     LLAKTKAWAD YDKAAAPLKA AIKKLAFSRA
//