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Database: UniProt/SWISS-PROT
Entry: DNLI1_ARATH
LinkDB: DNLI1_ARATH
Original site: DNLI1_ARATH 
ID   DNLI1_ARATH             Reviewed;         790 AA.
AC   Q42572; Q541Y6; Q56W81; Q9LMZ4; Q9SGE5;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   10-JAN-2003, sequence version 2.
DT   25-APR-2018, entry version 141.
DE   RecName: Full=DNA ligase 1;
DE            Short=AtLIG1;
DE            EC=6.5.1.1 {ECO:0000255|PROSITE-ProRule:PRU10135};
DE   AltName: Full=DNA ligase I;
DE   AltName: Full=Polydeoxyribonucleotide synthase [ATP] 1;
DE   Flags: Precursor;
GN   Name=LIG1; OrderedLocusNames=At1g08130; ORFNames=T23G18.1, T6D22.23;
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 [MRNA].
RC   STRAIN=cv. Landsberg erecta;
RX   PubMed=9681027; DOI=10.1046/j.1365-313X.1998.00094.x;
RA   Taylor R.M., Hamer M.J., Rosamond J., Bray C.M.;
RT   "Molecular cloning and functional analysis of the Arabidopsis thaliana
RT   DNA ligase I homologue.";
RL   Plant J. 14:75-81(1998).
RN   [2]
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   [3]
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   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=11910074; DOI=10.1126/science.1071006;
RA   Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA   Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M.,
RA   Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T.,
RA   Shibata K., Shinagawa A., Shinozaki K.;
RT   "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL   Science 296:141-145(2002).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=14593172; DOI=10.1126/science.1088305;
RA   Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J.,
RA   Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
RA   Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
RA   Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
RA   Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
RA   Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
RA   Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
RA   Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
RA   Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
RA   Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
RA   Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
RA   Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.;
RT   "Empirical analysis of transcriptional activity in the Arabidopsis
RT   genome.";
RL   Science 302:842-846(2003).
RN   [6]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 427-790.
RC   STRAIN=cv. Columbia;
RA   Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA   Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA   Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA   Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J.,
RA   Hayashizaki Y., Shinozaki K.;
RT   "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL   Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN   [7]
RP   IDENTIFICATION OF ISOFORMS 1; 2 AND 3, AND SUBCELLULAR LOCATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=16790030; DOI=10.1111/j.1365-313X.2006.02791.x;
RA   Sunderland P.A., West C.E., Waterworth W.M., Bray C.M.;
RT   "An evolutionarily conserved translation initiation mechanism
RT   regulates nuclear or mitochondrial targeting of DNA ligase 1 in
RT   Arabidopsis thaliana.";
RL   Plant J. 47:356-367(2006).
RN   [8]
RP   REVIEW.
RX   PubMed=17556508; DOI=10.1104/pp.107.101105;
RA   Shultz R.W., Tatineni V.M., Hanley-Bowdoin L., Thompson W.F.;
RT   "Genome-wide analysis of the core DNA replication machinery in the
RT   higher plants Arabidopsis and rice.";
RL   Plant Physiol. 144:1697-1714(2007).
RN   [9]
RP   FUNCTION, AND DISRUPTION PHENOTYPE.
RC   STRAIN=cv. Columbia;
RX   PubMed=19558640; DOI=10.1186/1471-2229-9-79;
RA   Waterworth W.M., Kozak J., Provost C.M., Bray C.M., Angelis K.J.,
RA   West C.E.;
RT   "DNA ligase 1 deficient plants display severe growth defects and
RT   delayed repair of both DNA single and double strand breaks.";
RL   BMC Plant Biol. 9:79-79(2009).
RN   [10]
RP   FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, AND DEVELOPMENTAL
RP   STAGE.
RX   PubMed=20023162; DOI=10.1242/dev.041020;
RA   Andreuzza S., Li J., Guitton A.-E., Faure J.-E., Casanova S.,
RA   Park J.-S., Choi Y., Chen Z., Berger F.;
RT   "DNA LIGASE I exerts a maternal effect on seed development in
RT   Arabidopsis thaliana.";
RL   Development 137:73-81(2010).
CC   -!- FUNCTION: Essential protein. DNA ligase that seals nicks in
CC       double-stranded DNA during DNA replication, DNA recombination and
CC       DNA repair. Involved in repair of both single strand breaks (SSBs)
CC       and double strand breaks (DSBs). Required in the endosperm for
CC       embryogenesis, probably to repair DNA-breaks generated by DME.
CC       {ECO:0000269|PubMed:19558640, ECO:0000269|PubMed:20023162}.
CC   -!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
CC       5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
CC       AMP + diphosphate. {ECO:0000255|PROSITE-ProRule:PRU10135}.
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC   -!- SUBCELLULAR LOCATION: Isoform 1: Mitochondrion.
CC   -!- SUBCELLULAR LOCATION: Isoform 2: Nucleus.
CC   -!- SUBCELLULAR LOCATION: Isoform 3: Nucleus.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative initiation; Named isoforms=3;
CC       Name=1;
CC         IsoId=Q42572-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q42572-2; Sequence=VSP_043694;
CC       Name=3;
CC         IsoId=Q42572-3; Sequence=VSP_043693;
CC   -!- TISSUE SPECIFICITY: Expressed in all vegetative and reproductive
CC       tissues. {ECO:0000269|PubMed:20023162}.
CC   -!- DEVELOPMENTAL STAGE: In the mature male gametophyte, expressed in
CC       the vegetative cell as well as in the two sperm cells. In the
CC       mature female gametes, accumulates in the embryo sac; mostly
CC       expressed in the central cell nucleus and, at lower levels, in the
CC       egg cell and synergids. After fertilization, localized in the
CC       syncytial endosperm and in the embryo.
CC       {ECO:0000269|PubMed:20023162}.
CC   -!- DISRUPTION PHENOTYPE: Lethal. {ECO:0000269|PubMed:19558640}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAF18258.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=AAF79833.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAD95276.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};
DR   EMBL; X97924; CAA66599.1; -; mRNA.
DR   EMBL; AC011438; AAF18258.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AC026875; AAF79833.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002684; AEE28251.1; -; Genomic_DNA.
DR   EMBL; AK117238; BAC41914.1; -; mRNA.
DR   EMBL; BT005964; AAO64899.1; -; mRNA.
DR   EMBL; AK222166; BAD95276.1; ALT_INIT; mRNA.
DR   PIR; S71278; S71278.
DR   RefSeq; NP_172293.2; NM_100689.5. [Q42572-1]
DR   UniGene; At.36; -.
DR   ProteinModelPortal; Q42572; -.
DR   SMR; Q42572; -.
DR   STRING; 3702.AT1G08130.1; -.
DR   iPTMnet; Q42572; -.
DR   PaxDb; Q42572; -.
DR   PRIDE; Q42572; -.
DR   EnsemblPlants; AT1G08130.1; AT1G08130.1; AT1G08130. [Q42572-1]
DR   GeneID; 837333; -.
DR   Gramene; AT1G08130.1; AT1G08130.1; AT1G08130. [Q42572-1]
DR   KEGG; ath:AT1G08130; -.
DR   Araport; AT1G08130; -.
DR   TAIR; locus:2199953; AT1G08130.
DR   eggNOG; KOG0967; Eukaryota.
DR   eggNOG; COG1793; LUCA.
DR   HOGENOM; HOG000036006; -.
DR   InParanoid; Q42572; -.
DR   KO; K10747; -.
DR   OMA; WIKYKRD; -.
DR   OrthoDB; EOG0936033M; -.
DR   PhylomeDB; Q42572; -.
DR   Reactome; R-ATH-174414; Processive synthesis on the C-strand of the telomere.
DR   Reactome; R-ATH-5358565; Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
DR   Reactome; R-ATH-5358606; Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
DR   Reactome; R-ATH-5651801; PCNA-Dependent Long Patch Base Excision Repair.
DR   Reactome; R-ATH-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR   Reactome; R-ATH-69183; Processive synthesis on the lagging strand.
DR   PRO; PR:Q42572; -.
DR   Proteomes; UP000006548; Chromosome 1.
DR   ExpressionAtlas; Q42572; baseline and differential.
DR   Genevisible; Q42572; AT.
DR   GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR   GO; GO:0005730; C:nucleolus; IDA:TAIR.
DR   GO; GO:0005634; C:nucleus; IDA:TAIR.
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:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR   GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR   GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro.
DR   GO; GO:0080111; P:DNA demethylation; IMP:TAIR.
DR   GO; GO:0051103; P:DNA ligation involved in DNA repair; IBA:GO_Central.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006260; P:DNA replication; IMP:UniProtKB.
DR   GO; GO:0006302; P:double-strand break repair; IMP:UniProtKB.
DR   GO; GO:0006273; P:lagging strand elongation; IBA:GO_Central.
DR   GO; GO:0000012; P:single strand break repair; IMP:UniProtKB.
DR   Gene3D; 1.10.3260.10; -; 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; IPR012340; NA-bd_OB-fold.
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   SUPFAM; SSF117018; SSF117018; 1.
DR   SUPFAM; SSF50249; SSF50249; 1.
DR   TIGRFAMs; TIGR00574; dnl1; 1.
DR   PROSITE; PS00697; DNA_LIGASE_A1; 1.
DR   PROSITE; PS00333; DNA_LIGASE_A2; 1.
DR   PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE   2: Evidence at transcript level;
KW   Alternative initiation; ATP-binding; Cell cycle; Cell division;
KW   Complete proteome; DNA damage; DNA recombination; DNA repair;
KW   DNA replication; Ligase; Magnesium; Metal-binding; Mitochondrion;
KW   Nucleotide-binding; Nucleus; Reference proteome; Repeat;
KW   Transit peptide.
FT   TRANSIT       1     64       Mitochondrion. {ECO:0000255}.
FT   CHAIN        65    790       DNA ligase 1.
FT                                /FTId=PRO_0000059586.
FT   REGION      337    346       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   REGION      518    520       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   MOTIF        68     75       Nuclear localization signal 1.
FT                                {ECO:0000250}.
FT   MOTIF       505    512       Nuclear localization signal 2.
FT                                {ECO:0000250}.
FT   ACT_SITE    444    444       N6-AMP-lysine intermediate.
FT                                {ECO:0000255|PROSITE-ProRule:PRU10135}.
FT   METAL       497    497       Magnesium 1. {ECO:0000250}.
FT   METAL       596    596       Magnesium 2. {ECO:0000250}.
FT   BINDING     442    442       ATP. {ECO:0000250}.
FT   BINDING     449    449       ATP. {ECO:0000250}.
FT   BINDING     465    465       ATP. {ECO:0000250}.
FT   BINDING     601    601       ATP. {ECO:0000250}.
FT   BINDING     614    614       ATP. {ECO:0000250}.
FT   BINDING     620    620       ATP. {ECO:0000250}.
FT   SITE        193    193       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   SITE        466    466       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   SITE        646    646       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   SITE        671    671       Interaction with target DNA.
FT                                {ECO:0000250}.
FT   VAR_SEQ       1     59       Missing (in isoform 3). {ECO:0000305}.
FT                                /FTId=VSP_043693.
FT   VAR_SEQ       1     47       Missing (in isoform 2). {ECO:0000305}.
FT                                /FTId=VSP_043694.
FT   CONFLICT    639    639       A -> P (in Ref. 1; CAA66599).
FT                                {ECO:0000305}.
SQ   SEQUENCE   790 AA;  87740 MW;  674EB9CAA9C5D329 CRC64;
     MLAIRSSNYL RCIPSLCTKT QISQFSSVLI SFSRQISHLR LSSCHRAMSS SRPSAFDALM
     SNARAAAKKK TPQTTNLSRS PNKRKIGETQ DANLGKTIVS EGTLPKTEDL LEPVSDSANP
     RSDTSSIAED SKTGAKKAKT LSKTDEMKSK IGLLKKKPND FDPEKMSCWE KGERVPFLFV
     ALAFDLISNE SGRIVITDIL CNMLRTVIAT TPEDLVATVY LSANEIAPAH EGVELGIGES
     TIIKAISEAF GRTEDHVKKQ NTELGDLGLV AKGSRSTQTM MFKPEPLTVV KVFDTFRQIA
     KESGKDSNEK KKNRMKALLV ATTDCEPLYL TRLLQAKLRL GFSGQTVLAA LGQAAVYNEE
     HSKPPPNTKS PLEEAAKIVK QVFTVLPVYD IIVPALLSGG VWNLPKTCNF TLGVPIGPML
     AKPTKGVAEI LNKFQDIVFT CEYKYDGERA QIHFMEDGTF EIYSRNAERN TGKYPDVALA
     LSRLKKPSVK SFILDCEVVA FDREKKKILP FQILSTRARK NVNVNDIKVG VCIFAFDMLY
     LNGQQLIQEN LKIRREKLYE SFEEDPGYFQ FATAVTSNDI DEIQKFLDAS VDVGCEGLII
     KTLDSDATYE PAKRSNNWLK LKKDYMDSIG DSVDLVPIAA FHGRGKRTGV YGAFLLACYD
     VDKEEFQSIC KIGTGFSDAM LDERSSSLRS QVIATPKQYY RVGDSLNPDV WFEPTEVWEV
     KAADLTISPV HRAATGIVDP DKGISLRFPR LLRVREDKKP EEATSSEQIA DLYQAQKHNH
     PSNEVKGDDD
//
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