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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   24-JAN-2024, entry version 167.
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; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; 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 DNA
RT   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., 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   [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 reference
RT   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., Hayashizaki Y.,
RA   Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA   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., Southwick A.M.,
RA   Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA   Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA   Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA   Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA   Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA   Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA   Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA   Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA   Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA   Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA   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., Hayashizaki Y.,
RA   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 regulates
RT   nuclear or mitochondrial targeting of DNA ligase 1 in Arabidopsis
RT   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 higher
RT   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 delayed
RT   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., Park J.-S.,
RA   Choi Y., Chen Z., Berger F.;
RT   "DNA LIGASE I exerts a maternal effect on seed development in Arabidopsis
RT   thaliana.";
RL   Development 137:73-81(2010).
CC   -!- FUNCTION: Essential protein. DNA ligase that seals nicks in double-
CC       stranded DNA during DNA replication, DNA recombination and DNA repair.
CC       Involved in repair of both single strand breaks (SSBs) and double
CC       strand breaks (DSBs). Required in the endosperm for embryogenesis,
CC       probably to repair DNA-breaks generated by DME.
CC       {ECO:0000269|PubMed:19558640, ECO:0000269|PubMed:20023162}.
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:0000255|PROSITE-
CC         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 the
CC       vegetative cell as well as in the two sperm cells. In the mature female
CC       gametes, accumulates in the embryo sac; mostly expressed in the central
CC       cell nucleus and, at lower levels, in the egg cell and synergids. After
CC       fertilization, localized in the 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=Truncated N-terminus.; Evidence={ECO:0000305};
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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   AlphaFoldDB; Q42572; -.
DR   SMR; Q42572; -.
DR   BioGRID; 22574; 1.
DR   STRING; 3702.Q42572; -.
DR   iPTMnet; Q42572; -.
DR   PaxDb; 3702-AT1G08130-1; -.
DR   ProteomicsDB; 222610; -. [Q42572-1]
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; AT1G08130; LIG1.
DR   eggNOG; KOG0967; Eukaryota.
DR   HOGENOM; CLU_005138_4_0_1; -.
DR   InParanoid; Q42572; -.
DR   OMA; WIKYKRD; -.
DR   OrthoDB; 961at2759; -.
DR   PhylomeDB; Q42572; -.
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; IEA:UniProtKB-EC.
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: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:0000012; P:single strand break repair; IMP:UniProtKB.
DR   CDD; cd07900; Adenylation_DNA_ligase_I_Euk; 1.
DR   CDD; cd07969; OBF_DNA_ligase_I; 1.
DR   Gene3D; 3.30.1490.70; -; 1.
DR   Gene3D; 1.10.3260.10; DNA ligase, ATP-dependent, N-terminal domain; 1.
DR   Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 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   NCBIfam; TIGR00574; dnl1; 1.
DR   PANTHER; PTHR45674:SF4; DNA LIGASE 1; 1.
DR   PANTHER; PTHR45674; DNA LIGASE 1/3 FAMILY MEMBER; 1.
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; ATP-dependent DNA ligase DNA-binding domain; 1.
DR   SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 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; DNA damage;
KW   DNA recombination; DNA repair; DNA replication; Ligase; Magnesium;
KW   Metal-binding; Mitochondrion; Nucleotide-binding; Nucleus;
KW   Reference proteome; Repeat; Transit peptide.
FT   TRANSIT         1..64
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000255"
FT   CHAIN           65..790
FT                   /note="DNA ligase 1"
FT                   /id="PRO_0000059586"
FT   REGION          64..142
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          337..346
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   REGION          518..520
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   REGION          757..790
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   MOTIF           68..75
FT                   /note="Nuclear localization signal 1"
FT                   /evidence="ECO:0000250"
FT   MOTIF           505..512
FT                   /note="Nuclear localization signal 2"
FT                   /evidence="ECO:0000250"
FT   COMPBIAS        67..83
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        444
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT   BINDING         442
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         449
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         465
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         497
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000250"
FT   BINDING         596
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000250"
FT   BINDING         601
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         614
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         620
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   SITE            193
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   SITE            466
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   SITE            646
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   SITE            671
FT                   /note="Interaction with target DNA"
FT                   /evidence="ECO:0000250"
FT   VAR_SEQ         1..59
FT                   /note="Missing (in isoform 3)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_043693"
FT   VAR_SEQ         1..47
FT                   /note="Missing (in isoform 2)"
FT                   /evidence="ECO:0000305"
FT                   /id="VSP_043694"
FT   CONFLICT        639
FT                   /note="A -> P (in Ref. 1; CAA66599)"
FT                   /evidence="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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