ID Q133M6_RHOPS Unreviewed; 930 AA.
AC Q133M6;
DT 31-OCT-2006, integrated into UniProtKB/TrEMBL.
DT 31-OCT-2006, sequence version 1.
DT 24-JAN-2024, entry version 90.
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 OMA; YMANLGC; -.
DR Proteomes; UP000001818; 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: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
//