LIG6_ARATH
ID LIG6_ARATH Reviewed; 1396 AA.
AC F4HPZ9; Q9C9M5;
DT 08-JUN-2016, integrated into UniProtKB/Swiss-Prot.
DT 28-JUN-2011, sequence version 1.
DT 03-AUG-2022, entry version 76.
DE RecName: Full=DNA ligase 6 {ECO:0000303|PubMed:20584150};
DE Short=AtLIG6 {ECO:0000303|PubMed:20584150};
DE Short=DNA ligase VI {ECO:0000303|PubMed:25641249};
DE EC=6.5.1.1 {ECO:0000250|UniProtKB:P56709, ECO:0000255|PROSITE-ProRule:PRU10135};
DE AltName: Full=Ligase 1 {ECO:0000303|PubMed:15155891};
GN Name=LIG6 {ECO:0000303|PubMed:20584150};
GN OrderedLocusNames=At1g66730 {ECO:0000312|Araport:AT1G66730};
GN ORFNames=F4N21.14 {ECO:0000312|EMBL:AAG60081.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130712; DOI=10.1038/35048500;
RA Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O.,
RA Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E.,
RA Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K., Conn L.,
RA Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P.,
RA Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D.,
RA Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J.,
RA Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L.,
RA Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A.,
RA Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A.,
RA Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M.,
RA Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M.,
RA Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P.,
RA Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D.,
RA Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D.,
RA Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana.";
RL Nature 408:816-820(2000).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP IDENTIFICATION.
RX PubMed=11948185; DOI=10.1074/jbc.m201411200;
RA Petrucco S., Volpi G., Bolchi A., Rivetti C., Ottonello S.;
RT "A nick-sensing DNA 3'-repair enzyme from Arabidopsis.";
RL J. Biol. Chem. 277:23675-23683(2002).
RN [4]
RP INDUCTION BY UV-C.
RC STRAIN=cv. Columbia;
RX PubMed=15155891; DOI=10.1105/tpc.021378;
RA Molinier J., Ramos C., Fritsch O., Hohn B.;
RT "CENTRIN2 modulates homologous recombination and nucleotide excision repair
RT in Arabidopsis.";
RL Plant Cell 16:1633-1643(2004).
RN [5]
RP FUNCTION, DISRUPTION PHENOTYPE, TISSUE SPECIFICITY, AND INDUCTION BY
RP IMBIBITION.
RC STRAIN=cv. Columbia;
RX PubMed=20584150; DOI=10.1111/j.1365-313x.2010.04285.x;
RA Waterworth W.M., Masnavi G., Bhardwaj R.M., Jiang Q., Bray C.M., West C.E.;
RT "A plant DNA ligase is an important determinant of seed longevity.";
RL Plant J. 63:848-860(2010).
RN [6]
RP INDUCTION BY BLEOMYCIN.
RX PubMed=26074930; DOI=10.3389/fpls.2015.00357;
RA Furukawa T., Angelis K.J., Britt A.B.;
RT "Arabidopsis DNA polymerase lambda mutant is mildly sensitive to DNA double
RT strand breaks but defective in integration of a transgene.";
RL Front. Plant Sci. 6:357-357(2015).
RN [7]
RP FUNCTION, AND DISRUPTION PHENOTYPE.
RC STRAIN=cv. Columbia;
RX PubMed=25641249; DOI=10.1111/tpj.12779;
RA Park S.-Y., Vaghchhipawala Z., Vasudevan B., Lee L.-Y., Shen Y., Singer K.,
RA Waterworth W.M., Zhang Z.J., West C.E., Mysore K.S., Gelvin S.B.;
RT "Agrobacterium T-DNA integration into the plant genome can occur without
RT the activity of key non-homologous end-joining proteins.";
RL Plant J. 81:934-946(2015).
CC -!- FUNCTION: DNA ligase that seals nicks in double-stranded DNA during DNA
CC replication, DNA recombination and DNA repair (Probable). Required to
CC maintain seed viability (e.g. longevity and storability) and during
CC seed germination, probably by repairing DNA damage accumulated during
CC seed development, storage and/or imbibition. Facilitates seed
CC germination in cold conditions (2 degrees Celsius) and under oxidative
CC stress (e.g. menadione, a genotoxic agent). Involved in repair of X-
CC ray-induced damage (PubMed:20584150). {ECO:0000269|PubMed:20584150,
CC ECO:0000305}.
CC -!- FUNCTION: Limits stable root transformation by A.tumefaciens T-DNA.
CC {ECO:0000269|PubMed:25641249}.
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:0000250|UniProtKB:P56709,
CC ECO:0000255|PROSITE-ProRule:PRU10135};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P56709};
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000255|PROSITE-ProRule:PRU00768}.
CC -!- TISSUE SPECIFICITY: Mostly expressed in buds and flowers, and, to a
CC lower extent, in stems, leaves, siliques and seeds.
CC {ECO:0000269|PubMed:20584150}.
CC -!- INDUCTION: Induced by UV-C (PubMed:15155891). Induced during seed
CC imbibition (PubMed:20584150). Induced slightly by bleomycin (BLM), a
CC radiomimetic reagent that generates DNA double-strand breaks (DSBs)
CC (PubMed:26074930). {ECO:0000269|PubMed:15155891,
CC ECO:0000269|PubMed:20584150, ECO:0000269|PubMed:26074930}.
CC -!- DISRUPTION PHENOTYPE: Normal vegetative growth and fertility. Slightly
CC enhanced sensitivity to X-rays, leading to a slight root growth
CC reduction after 100-Gy dose of X-ray irradiation. Delayed germination
CC of seeds, especially upon cold and oxidative stress (e.g. by menadione,
CC a genotoxic agent), and reduced seed longevity and storability.
CC Increased DNA damage response in germinating seeds, probably due to
CC accumulation of DNA damage in seeds (PubMed:20584150). Increased stable
CC root transformation susceptibility by A.tumefaciens A208 T-DNA
CC (PubMed:25641249). {ECO:0000269|PubMed:20584150,
CC ECO:0000269|PubMed:25641249}.
CC -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAG60081.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC013288; AAG60081.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002684; AEE34549.1; -; Genomic_DNA.
DR RefSeq; NP_176845.2; NM_105343.3.
DR AlphaFoldDB; F4HPZ9; -.
DR SMR; F4HPZ9; -.
DR STRING; 3702.AT1G66730.1; -.
DR iPTMnet; F4HPZ9; -.
DR PaxDb; F4HPZ9; -.
DR PRIDE; F4HPZ9; -.
DR ProteomicsDB; 238450; -.
DR EnsemblPlants; AT1G66730.1; AT1G66730.1; AT1G66730.
DR GeneID; 842991; -.
DR Gramene; AT1G66730.1; AT1G66730.1; AT1G66730.
DR KEGG; ath:AT1G66730; -.
DR Araport; AT1G66730; -.
DR TAIR; locus:2033374; AT1G66730.
DR eggNOG; KOG0967; Eukaryota.
DR eggNOG; KOG1361; Eukaryota.
DR HOGENOM; CLU_005138_3_0_1; -.
DR InParanoid; F4HPZ9; -.
DR OMA; HVTGWNI; -.
DR OrthoDB; 274264at2759; -.
DR BRENDA; 6.5.1.1; 399.
DR PRO; PR:F4HPZ9; -.
DR Proteomes; UP000006548; Chromosome 1.
DR ExpressionAtlas; F4HPZ9; baseline and differential.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005634; C:nucleus; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro.
DR GO; GO:0015074; P:DNA integration; IMP:UniProtKB.
DR GO; GO:0006266; P:DNA ligation; IBA:GO_Central.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006281; P:DNA repair; IMP:UniProtKB.
DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IMP:TAIR.
DR GO; GO:0006273; P:lagging strand elongation; IBA:GO_Central.
DR GO; GO:2000685; P:positive regulation of cellular response to X-ray; IMP:UniProtKB.
DR GO; GO:1904975; P:response to bleomycin; IEP:UniProtKB.
DR GO; GO:0009409; P:response to cold; IMP:UniProtKB.
DR GO; GO:0002237; P:response to molecule of bacterial origin; IMP:UniProtKB.
DR GO; GO:0006979; P:response to oxidative stress; IMP:UniProtKB.
DR GO; GO:0010225; P:response to UV-C; IDA:UniProtKB.
DR GO; GO:0048316; P:seed development; IMP:UniProtKB.
DR GO; GO:0009845; P:seed germination; IMP:TAIR.
DR Gene3D; 1.10.3260.10; -; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.60.15.10; -; 1.
DR InterPro; IPR000977; DNA_ligase_ATP-dep.
DR InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR InterPro; IPR016059; DNA_ligase_ATP-dep_CS.
DR InterPro; IPR012308; DNA_ligase_ATP-dep_N.
DR InterPro; IPR036599; DNA_ligase_N_sf.
DR InterPro; IPR011084; DRMBL.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR036866; RibonucZ/Hydroxyglut_hydro.
DR Pfam; PF04679; DNA_ligase_A_C; 1.
DR Pfam; PF01068; DNA_ligase_A_M; 1.
DR Pfam; PF04675; DNA_ligase_A_N; 1.
DR Pfam; PF07522; DRMBL; 1.
DR SUPFAM; SSF117018; SSF117018; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF56281; SSF56281; 1.
DR TIGRFAMs; TIGR00574; dnl1; 1.
DR PROSITE; PS00697; DNA_LIGASE_A1; 1.
DR PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; DNA damage; DNA recombination; DNA repair; DNA replication;
KW Ligase; Magnesium; Metal-binding; Nucleotide-binding; Nucleus;
KW Reference proteome.
FT CHAIN 1..1396
FT /note="DNA ligase 6"
FT /evidence="ECO:0000255"
FT /id="PRO_0000436440"
FT REGION 441..464
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 562..599
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOTIF 572..579
FT /note="Nuclear localization signal 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT MOTIF 886..893
FT /note="Nuclear localization signal 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00768"
FT ACT_SITE 1039
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P56709,
FT ECO:0000255|PROSITE-ProRule:PRU10135"
FT BINDING 1037
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P56709"
FT BINDING 1044
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P56709"
FT BINDING 1060
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P56709"
FT BINDING 1092
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P56709"
FT BINDING 1092
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P18858"
FT BINDING 1136
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P56709"
FT BINDING 1207
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P18858"
FT BINDING 1212
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P18858"
FT BINDING 1225
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 1231
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P56709"
SQ SEQUENCE 1396 AA; 156322 MW; 551005493C22FFC9 CRC64;
MASDSAGATI SGNFSNSDNS ETLNLNTTKL YSSAISSISP QFPSPKPTSS CPSIPNSKRI
PNTNFIVDLF RLPHQSSSVA FFLSHFHSDH YSGLSSSWSK GIIYCSHKTA RLVAEILQVP
SQFVFALPMN QMVKIDGSEV VLIEANHCPG AVQFLFKVKL ESSGFEKYVH TGDFRFCDEM
RFDPFLNGFV GCDGVFLDTT YCNPKFVFPS QEESVGYVVS VIDKISEEKV LFLVATYVVG
KEKILVEIAR RCKRKIVVDA RKMSMLSVLG CGEEGMFTED ENESDVHVVG WNVLGETWPY
FRPNFVKMNE IMVEKGYDKV VGFVPTGWTY EVKRNKFAVR FKDSMEIHLV PYSEHSNYDE
LREFIKFLKP KRVIPTVGVD IEKFDCKEVN KMQKHFSGLV DEMANKKDFL LGFYRQSYQK
NEKSDVDVVS HSAEVYEEEE KNACEDGGEN VPSSRGPILH DTTPSSDSRL LIKLRDSLPA
WVTEEQMLDL IKKHAGNPVD IVSNFYEYEA ELYKQASLPT PSLNNQAVLF DDDVTDLQPN
PVKGICPDVQ AIQKGFDLPR KMNLTKGTIS PGKRGKSSGS KSNKKAKKDP KSKPVGPGQP
TLFKFFNKVL DGGSNSVSVG SETEECNTDK KMVHIDASEA YKEVTDQFID IVNGSESLRD
YAASIIDEAK GDISRALNIY YSKPREIPGD HAGERGLSSK TIQYPKCSEA CSSQEDKKAS
ENSGHAVNIC VQTSAEESVD KNYVSLPPEK YQPKEHACWR EGQPAPYIHL VRTFASVESE
KGKIKAMSML CNMFRSLFAL SPEDVLPAVY LCTNKIAADH ENIELNIGGS LISSALEEAC
GISRSTVRDM YNSLGDLGDV AQLCRQTQKL LVPPPPLLVR DVFSTLRKIS VQTGTGSTRL
KKNLIVKLMR SCREKEIKFL VRTLARNLRI GAMLRTVLPA LGRAIVMNSF WNDHNKELSE
SCFREKLEGV SAAVVEAYNI LPSLDVVVPS LMDKDIEFST STLSMVPGIP IKPMLAKIAK
GVQEFFNLSQ EKAFTCEYKY DGQRAQIHKL LDGTVCIFSR NGDETTSRFP DLVDVIKQFS
CPAAETFMLD AEVVATDRIN GNKLMSFQEL STRERGSKDA LITTESIKVE VCVFVFDIMF
VNGEQLLALP LRERRRRLKE VFPETRPGYL EYAKEITVGA EEASLNNHDT LSRINAFLEE
AFQSSCEGIM VKSLDVNAGY CPTKRSDSWL KVKRDYVDGL GDTLDLVPIG AWYGNGRKAG
WYSPFLMACF NPETEEFQSV CRVMSGFSDA FYIEMKEFYS EDKILAKKPP YYRTGETPDM
WFSAEVVWEI RGADFTVSPV HSASLGLVHP SRGISVRFPR FISKVTDRNP EECSTATDIA
EMFHAQTRKM NITSQH
