GenomeNet

Database: UniProt/SWISS-PROT
Entry: LIG6_ARATH
LinkDB: LIG6_ARATH
Original site: 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   08-MAY-2019, entry version 62.
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; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   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.,
RA   White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y.,
RA   Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W.,
RA   Chung M.K., Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K.,
RA   Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y.,
RA   Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L.,
RA   Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E.,
RA   Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B.,
RA   Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P.,
RA   Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A.,
RA   Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I.,
RA   Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D.,
RA   Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M.,
RA   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.,
RA   Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.;
RT   "Sequence and analysis of chromosome 1 of the plant Arabidopsis
RT   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
RT   reference 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
RT   repair 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.,
RA   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
RT   double 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.,
RA   Singer K., Waterworth W.M., Zhang Z.J., West C.E., Mysore K.S.,
RA   Gelvin S.B.;
RT   "Agrobacterium T-DNA integration into the plant genome can occur
RT   without 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
CC       during DNA replication, DNA recombination and DNA repair
CC       (Probable). Required to maintain seed viability (e.g. longevity
CC       and storability) and during seed germination, probably by
CC       repairing DNA damage accumulated during seed development, storage
CC       and/or imbibition. Faciliates seed germination in cold conditions
CC       (2 degrees Celsius) and under oxidative stress (e.g. menadione, a
CC       genotoxic agent). Involved in repair of X-ray-induced damage
CC       (PubMed:20584150). {ECO:0000269|PubMed:20584150, ECO:0000305}.
CC   -!- FUNCTION: Limits stable root transformation by A.tumefaciens T-
CC       DNA. {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;
CC         Evidence={ECO:0000250|UniProtKB:P56709, ECO:0000255|PROSITE-
CC         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-
CC       ProRule:PRU00768}.
CC   -!- TISSUE SPECIFICITY: Mostly expressed in buds and flowers, and, to
CC       a 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),
CC       a radiomimetic reagent that generates DNA double-strand breaks
CC       (DSBs) (PubMed:26074930). {ECO:0000269|PubMed:15155891,
CC       ECO:0000269|PubMed:20584150, ECO:0000269|PubMed:26074930}.
CC   -!- DISRUPTION PHENOTYPE: Normal vegetative growth and fertility.
CC       Slightly enhanced sensitivity to X-rays, leading to a slight root
CC       growth reduction after 100-Gy dose of X-ray irradiation. Delayed
CC       germination of seeds, especially upon cold and oxidative stress
CC       (e.g. by menadione, a genotoxic agent), and reduced seed longevity
CC       and storability. Increased DNA damage response in germinating
CC       seeds, probably due to accumulation of DNA damage in seeds
CC       (PubMed:20584150). Increased stable root transformation
CC       susceptibility by A.tumefaciens A208 T-DNA (PubMed:25641249).
CC       {ECO:0000269|PubMed:20584150, 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};
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   SMR; F4HPZ9; -.
DR   STRING; 3702.AT1G66730.1; -.
DR   iPTMnet; F4HPZ9; -.
DR   PaxDb; F4HPZ9; -.
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   eggNOG; COG1236; LUCA.
DR   eggNOG; COG1793; LUCA.
DR   HOGENOM; HOG000082752; -.
DR   InParanoid; F4HPZ9; -.
DR   OMA; RMNTFFK; -.
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:0005739; C:mitochondrion; IBA:GO_Central.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
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:0051103; P:DNA ligation involved in DNA repair; IEA:InterPro.
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; 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; Complete proteome; DNA damage; DNA recombination;
KW   DNA repair; DNA replication; Ligase; Magnesium; Metal-binding;
KW   Nucleotide-binding; Nucleus; Reference proteome.
FT   CHAIN         1   1396       DNA ligase 6. {ECO:0000255}.
FT                                /FTId=PRO_0000436440.
FT   MOTIF       572    579       Nuclear localization signal 1.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00768}.
FT   MOTIF       886    893       Nuclear localization signal 2.
FT                                {ECO:0000255|PROSITE-ProRule:PRU00768}.
FT   COMPBIAS      3     99       Ser-rich. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00016}.
FT   ACT_SITE   1039   1039       N6-AMP-lysine intermediate.
FT                                {ECO:0000250|UniProtKB:P56709,
FT                                ECO:0000255|PROSITE-ProRule:PRU10135}.
FT   METAL      1092   1092       Magnesium 1.
FT                                {ECO:0000250|UniProtKB:P18858}.
FT   METAL      1207   1207       Magnesium 2.
FT                                {ECO:0000250|UniProtKB:P18858}.
FT   BINDING    1037   1037       ATP. {ECO:0000250|UniProtKB:P56709}.
FT   BINDING    1044   1044       ATP. {ECO:0000250|UniProtKB:P56709}.
FT   BINDING    1060   1060       ATP. {ECO:0000250|UniProtKB:P56709}.
FT   BINDING    1092   1092       ATP. {ECO:0000250|UniProtKB:P56709}.
FT   BINDING    1136   1136       ATP. {ECO:0000250|UniProtKB:P56709}.
FT   BINDING    1212   1212       ATP. {ECO:0000250|UniProtKB:P18858}.
FT   BINDING    1225   1225       ATP. {ECO:0000250}.
FT   BINDING    1231   1231       ATP. {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
//
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