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 03-AUG-2022, entry version 160.
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.AT1G08130.1; -.
DR iPTMnet; Q42572; -.
DR PaxDb; Q42572; -.
DR PRIDE; Q42572; -.
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; locus:2199953; AT1G08130.
DR eggNOG; KOG0967; Eukaryota.
DR HOGENOM; CLU_005138_4_0_1; -.
DR InParanoid; Q42572; -.
DR OMA; WIKYKRD; -.
DR OrthoDB; 274264at2759; -.
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:0005737; C:cytoplasm; IBA:GO_Central.
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:0006266; P:DNA ligation; 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 Gene3D; 2.40.50.140; -; 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; 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
