ID C6VYF5_DYAFD Unreviewed; 902 AA.
AC C6VYF5;
DT 22-SEP-2009, integrated into UniProtKB/TrEMBL.
DT 22-SEP-2009, sequence version 1.
DT 27-MAR-2024, entry version 72.
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=Dfer_0365 {ECO:0000313|EMBL:ACT91634.1};
OS Dyadobacter fermentans (strain ATCC 700827 / DSM 18053 / CIP 107007 / KCTC
OS 52180 / NS114).
OC Bacteria; Bacteroidota; Cytophagia; Cytophagales; Spirosomataceae;
OC Dyadobacter.
OX NCBI_TaxID=471854 {ECO:0000313|EMBL:ACT91634.1, ECO:0000313|Proteomes:UP000002011};
RN [1] {ECO:0000313|EMBL:ACT91634.1, ECO:0000313|Proteomes:UP000002011}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700827 / DSM 18053 / CIP 107007 / KCTC 52180 / NS114
RC {ECO:0000313|Proteomes:UP000002011};
RX PubMed=21304649; DOI=10.4056/sigs.19262;
RA Lang E., Lapidus A., Chertkov O., Brettin T., Detter J.C., Han C.,
RA Copeland A., Glavina Del Rio T., Nolan M., Chen F., Lucas S., Tice H.,
RA Cheng J.F., Land M., Hauser L., Chang Y.J., Jeffries C.D., Kopitz M.,
RA Bruce D., Goodwin L., Pitluck S., Ovchinnikova G., Pati A., Ivanova N.,
RA Mavrommatis K., Chen A., Palaniappan K., Chain P., Bristow J., Eisen J.A.,
RA Markowitz V., Hugenholtz P., Goker M., Rohde M., Kyrpides N.C., Klenk H.P.;
RT "Complete genome sequence of Dyadobacter fermentans type strain (NS114).";
RL Stand. Genomic Sci. 1:133-140(2009).
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; CP001619; ACT91634.1; -; Genomic_DNA.
DR RefSeq; WP_012779982.1; NC_013037.1.
DR AlphaFoldDB; C6VYF5; -.
DR STRING; 471854.Dfer_0365; -.
DR KEGG; dfe:Dfer_0365; -.
DR eggNOG; COG1793; Bacteria.
DR eggNOG; COG3285; Bacteria.
DR HOGENOM; CLU_008325_0_2_10; -.
DR OrthoDB; 9802472at2; -.
DR Proteomes; UP000002011; 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; cd04865; LigD_Pol_like_2; 1.
DR CDD; cd07971; OBF_DNA_ligase_LigD; 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 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:ACT91634.1};
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:UP000002011};
KW Transferase {ECO:0000256|ARBA:ARBA00022679}.
FT DOMAIN 347..480
FT /note="ATP-dependent DNA ligase family profile"
FT /evidence="ECO:0000259|PROSITE:PS50160"
FT REGION 1..26
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 203..237
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 902 AA; 102392 MW; 0FF0F690B157578E CRC64;
MTLSKYNEKR KFDKTPEPKG GKGDNDELIF VIQKHDATRL HYDFRLEMEG VLKSWAVPKG
PSTDPSVKRL AMMVEDHPYD YKDFEGIIPK GNYGAGTVMV WDFGTYEPLE EVNGKLKAVK
GKKAREKLAL KELHSGSLKV RLNGKKVKGE YALVKTKGME ENAWLLIKHR DKYASEDDIT
EKDRSAVSRR TLAGIEKAGD AIWESNHEEK KSTKGKTKAA KTEAKDPAEE AATEKKSPDE
DIAAILKKGK KQKFPDDLQP MLATLVDGPF DDPGWEYEVK WDGYRALAYL NNGEVKLQSR
NRKSFSDKFY PIYQQLQEWK INAVIDGEIV VINDKGLSDF NALQNWRSEA DGELVYYAFD
IVWLEGKSLI HLPLSERKAI LKSIVDENSP VQLGYSVEAD GTAFFEAAQK MGLEGIMAKK
SDSEYYPGLR TRDWLKIKIN KRQEVIIAGY TLNEGSSKLF SALLLAAYAD GELQYVGKVG
TGFKEKQQKE MMALFKPLIA KKSPFKETPD YNKPSRFRPN PPHANATWLK PELVCEISFT
EITADGVFRH PSFEGMREDK SAKEVVREVE KPAEEIVDDA NEQSETIIRK PGRAKRKTLL
NPKEETQVRK ISGHEVKFSN LGKLYWPDDK IQKRELINYY YQVAPLILPY LENRPLSLNR
FPNGIRGKSF YQKDVTGKVP EWIETTPYVS EGENKNFMLC NDEATLLYMA NLGAIDVNPW
NSRIETPDNP DWCLLDLDPD TTNTFEQVIE TAQAIKNLLD SLGVPSYCKT SGSTGLHIYI
PLGAKYSYDQ CQLFAEWVAG QVQQQLPDFT SVERLTKNRK GKLYIDYLQN RPKATLAAPY
SVRPKPGATV SMPLHWEEVK VGLQLKDFTI YNAMDRIQRE GDLFKPVLGE GIDLEEVIAK
MG
//
