ID A0A0A7PKR9_9SPHN Unreviewed; 835 AA.
AC A0A0A7PKR9;
DT 04-MAR-2015, integrated into UniProtKB/TrEMBL.
DT 04-MAR-2015, sequence version 1.
DT 27-MAR-2024, entry version 39.
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 ORFNames=SKP52_18625 {ECO:0000313|EMBL:AJA10595.1};
OS Sphingopyxis fribergensis.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingopyxis.
OX NCBI_TaxID=1515612 {ECO:0000313|EMBL:AJA10595.1, ECO:0000313|Proteomes:UP000030907};
RN [1] {ECO:0000313|EMBL:AJA10595.1, ECO:0000313|Proteomes:UP000030907}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Kp5.2 {ECO:0000313|EMBL:AJA10595.1,
RC ECO:0000313|Proteomes:UP000030907};
RX PubMed=26040579; DOI=10.1099/ijs.0.000371;
RA Oelschlagel M., Ruckert C., Kalinowski J., Schmidt G., Schlomann M.,
RA Tischler D.;
RT "Description of Sphingopyxis fribergensis sp. nov. - a soil bacterium with
RT the ability to degrade styrene and phenylacetic acid.";
RL Int. J. Syst. Evol. Microbiol. 65:3008-3015(2015).
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; CP009122; AJA10595.1; -; Genomic_DNA.
DR RefSeq; WP_039577220.1; NZ_CP009122.1.
DR AlphaFoldDB; A0A0A7PKR9; -.
DR STRING; 1515612.SKP52_18625; -.
DR KEGG; sphk:SKP52_18625; -.
DR HOGENOM; CLU_008325_0_2_5; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000030907; 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; 3.30.470.30; 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:AJA10595.1};
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 330..421
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 532..555
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 835 AA; 91343 MW; 318D94930760A8B8 CRC64;
MPRAADPLAQ YNAKRDFALT PEPAGKVEKG AGNRFIVQKH DATRLHYDLR LEVDGVLKSW
AVTKGPSPDP ADKRLAVRTE DHPMSYADFE GGIPKGEYGG GTVMLWDRGT WAPIAGKSAK
DIDQGHLHFT LDGTRMKGEW LLVRMKPRPG EKRENWLLRK VDDAFAGGTD DLVGRELTSI
LTGRTMAEIA GDEGGEQSLK GAKGATFAKK MADAAAHNKK IAKPAAKGKL PKFRPLQLAT
LVDAVPGGNG WFHEIKYDGY RAEIAAAGSD VRIYTRNGLD WTDKFAPLVR HIAALDLPPC
LIDGEIVAYG KDGNPDFSSL QAVLKRGHGA QDEGTALHLF AFDLLELGGK SLANLGNLER
KERLEALLRD AKAPIAVADH VIGAGEKLYE AMCRAGQEGI ISKRADAGYS GRRSKNWLKV
KCTRRQEFIL VGWNPSSAKA RPFASLLLAQ REGDTLIYKG NVGTGFDSDT MADLAKKFAR
LERKTAPLDV DAAAARKVHW LRPELVAEIA FAEFTASGSV RHASFLGLRS DKEAKDVTPE
KKQPTPTPES DVTISSRDRV IFPEAKATKG DLADYYGAIA PVMLPHAARR PISLVRCPQG
RGKKCFFQKH DSGSFGDHVL HVPIKEKDGG HEDYLYVEDA DGLLACVQMG TIEFHGWGSH
VDSLEKPDRM VFDLDPDEGL DFADVKKAAL DIRRQLADIG LVSFAMLSGG KGVHVVVPLD
PGHSWDKHKD FSKRFAEALS MAEPDRFIAT MSKAKRKGKI FIDYLRNQRG STAVMPYSAR
AREQAPVAVP IGWDALADVE KAGQWTIKDS DELLARAVGP ELKGWGFANQ TLPDF
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