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Q42572

- DNLI1_ARATH

UniProt

Q42572 - DNLI1_ARATH

Protein

DNA ligase 1

Gene

LIG1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 113 (01 Oct 2014)
      Sequence version 2 (10 Jan 2003)
      Previous versions | rss
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    Functioni

    Essential protein. DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. Involved in repair of both single strand breaks (SSBs) and double strand breaks (DSBs). Required in the endosperm for embryogenesis, probably to repair DNA-breaks generated by DME.2 Publications

    Catalytic activityi

    ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).PROSITE-ProRule annotation

    Cofactori

    Magnesium.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sitei193 – 1931Interaction with target DNABy similarity
    Binding sitei442 – 4421ATPBy similarity
    Active sitei444 – 4441N6-AMP-lysine intermediatePROSITE-ProRule annotation
    Binding sitei449 – 4491ATPBy similarity
    Binding sitei465 – 4651ATPBy similarity
    Sitei466 – 4661Interaction with target DNABy similarity
    Metal bindingi497 – 4971Magnesium 1By similarity
    Metal bindingi596 – 5961Magnesium 2By similarity
    Binding sitei601 – 6011ATPBy similarity
    Binding sitei614 – 6141ATPBy similarity
    Binding sitei620 – 6201ATPBy similarity
    Sitei646 – 6461Interaction with target DNABy similarity
    Sitei671 – 6711Interaction with target DNABy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. DNA binding Source: InterPro
    3. DNA ligase (ATP) activity Source: RefGenome
    4. metal ion binding Source: UniProtKB-KW

    GO - Biological processi

    1. cell cycle Source: UniProtKB-KW
    2. cell division Source: UniProtKB-KW
    3. DNA ligation Source: RefGenome
    4. DNA ligation involved in DNA repair Source: InterPro
    5. DNA recombination Source: UniProtKB-KW
    6. DNA replication Source: UniProtKB
    7. double-strand break repair Source: UniProtKB
    8. single strand break repair Source: UniProtKB

    Keywords - Molecular functioni

    Ligase

    Keywords - Biological processi

    Cell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication

    Keywords - Ligandi

    ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciARA:AT1G08130-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA ligase 1 (EC:6.5.1.1)
    Short name:
    AtLIG1
    Alternative name(s):
    DNA ligase I
    Polydeoxyribonucleotide synthase [ATP] 1
    Gene namesi
    Name:LIG1
    Ordered Locus Names:At1g08130
    ORF Names:T23G18.1, T6D22.23
    OrganismiArabidopsis thaliana (Mouse-ear cress)
    Taxonomic identifieri3702 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
    ProteomesiUP000006548: Chromosome 1

    Organism-specific databases

    TAIRiAT1G08130.

    Subcellular locationi

    GO - Cellular componenti

    1. mitochondrion Source: TAIR
    2. nucleus Source: TAIR

    Keywords - Cellular componenti

    Mitochondrion, Nucleus

    Pathology & Biotechi

    Disruption phenotypei

    Lethal.1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Transit peptidei1 – 6464MitochondrionSequence AnalysisAdd
    BLAST
    Chaini65 – 790726DNA ligase 1PRO_0000059586Add
    BLAST

    Proteomic databases

    PaxDbiQ42572.
    PRIDEiQ42572.

    Expressioni

    Tissue specificityi

    Expressed in all vegetative and reproductive tissues.1 Publication

    Developmental stagei

    In the mature male gametophyte, expressed in the vegetative cell as well as in the two sperm cells. In the mature female gametes, accumulates in the embryo sac; mostly expressed in the central cell nucleus and, at lower levels, in the egg cell and synergids. After fertilization, localized in the syncytial endosperm and in the embryo.1 Publication

    Gene expression databases

    GenevestigatoriQ42572.

    Interactioni

    Protein-protein interaction databases

    STRINGi3702.AT1G08130.1-P.

    Structurei

    3D structure databases

    ProteinModelPortaliQ42572.
    SMRiQ42572. Positions 159-776.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni337 – 34610Interaction with target DNABy similarity
    Regioni518 – 5203Interaction with target DNABy similarity

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi68 – 758Nuclear localization signal 1By similarity
    Motifi505 – 5128Nuclear localization signal 2By similarity

    Sequence similaritiesi

    Belongs to the ATP-dependent DNA ligase family.Curated

    Keywords - Domaini

    Repeat, Transit peptide

    Phylogenomic databases

    eggNOGiCOG1793.
    HOGENOMiHOG000036006.
    InParanoidiQ42572.
    KOiK10747.
    OMAiMVKMLEG.
    PhylomeDBiQ42572.

    Family and domain databases

    Gene3Di1.10.3260.10. 1 hit.
    2.40.50.140. 1 hit.
    InterProiIPR000977. DNA_ligase_ATP-dep.
    IPR012309. DNA_ligase_ATP-dep_C.
    IPR012310. DNA_ligase_ATP-dep_cent.
    IPR016059. DNA_ligase_ATP-dep_CS.
    IPR012308. DNA_ligase_ATP-dep_N.
    IPR012340. NA-bd_OB-fold.
    [Graphical view]
    PfamiPF04679. DNA_ligase_A_C. 1 hit.
    PF01068. DNA_ligase_A_M. 1 hit.
    PF04675. DNA_ligase_A_N. 1 hit.
    [Graphical view]
    SUPFAMiSSF117018. SSF117018. 1 hit.
    SSF50249. SSF50249. 1 hit.
    TIGRFAMsiTIGR00574. dnl1. 1 hit.
    PROSITEiPS00697. DNA_LIGASE_A1. 1 hit.
    PS00333. DNA_LIGASE_A2. 1 hit.
    PS50160. DNA_LIGASE_A3. 1 hit.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 3 isoformsi produced by alternative initiation. Align

    Isoform 1 (identifier: Q42572-1) [UniParc]FASTAAdd to Basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

    MLAIRSSNYL RCIPSLCTKT QISQFSSVLI SFSRQISHLR LSSCHRAMSS    50
    SRPSAFDALM SNARAAAKKK TPQTTNLSRS PNKRKIGETQ DANLGKTIVS 100
    EGTLPKTEDL LEPVSDSANP RSDTSSIAED SKTGAKKAKT LSKTDEMKSK 150
    IGLLKKKPND FDPEKMSCWE KGERVPFLFV ALAFDLISNE SGRIVITDIL 200
    CNMLRTVIAT TPEDLVATVY LSANEIAPAH EGVELGIGES TIIKAISEAF 250
    GRTEDHVKKQ NTELGDLGLV AKGSRSTQTM MFKPEPLTVV KVFDTFRQIA 300
    KESGKDSNEK KKNRMKALLV ATTDCEPLYL TRLLQAKLRL GFSGQTVLAA 350
    LGQAAVYNEE HSKPPPNTKS PLEEAAKIVK QVFTVLPVYD IIVPALLSGG 400
    VWNLPKTCNF TLGVPIGPML AKPTKGVAEI LNKFQDIVFT CEYKYDGERA 450
    QIHFMEDGTF EIYSRNAERN TGKYPDVALA LSRLKKPSVK SFILDCEVVA 500
    FDREKKKILP FQILSTRARK NVNVNDIKVG VCIFAFDMLY LNGQQLIQEN 550
    LKIRREKLYE SFEEDPGYFQ FATAVTSNDI DEIQKFLDAS VDVGCEGLII 600
    KTLDSDATYE PAKRSNNWLK LKKDYMDSIG DSVDLVPIAA FHGRGKRTGV 650
    YGAFLLACYD VDKEEFQSIC KIGTGFSDAM LDERSSSLRS QVIATPKQYY 700
    RVGDSLNPDV WFEPTEVWEV KAADLTISPV HRAATGIVDP DKGISLRFPR 750
    LLRVREDKKP EEATSSEQIA DLYQAQKHNH PSNEVKGDDD 790
    Length:790
    Mass (Da):87,740
    Last modified:January 10, 2003 - v2
    Checksum:i674EB9CAA9C5D329
    GO
    Isoform 2 (identifier: Q42572-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-47: Missing.

    Show »
    Length:743
    Mass (Da):82,417
    Checksum:iD7DCE08F0DBC0C4D
    GO
    Isoform 3 (identifier: Q42572-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-59: Missing.

    Show »
    Length:731
    Mass (Da):81,167
    Checksum:i72E76F2F2A57830B
    GO

    Sequence cautioni

    The sequence BAD95276.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.
    The sequence AAF18258.1 differs from that shown. Reason: Erroneous gene model prediction.
    The sequence AAF79833.1 differs from that shown. Reason: Erroneous gene model prediction.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti639 – 6391A → P in CAA66599. (PubMed:9681027)Curated

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 5959Missing in isoform 3. CuratedVSP_043693Add
    BLAST
    Alternative sequencei1 – 4747Missing in isoform 2. CuratedVSP_043694Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X97924 mRNA. Translation: CAA66599.1.
    AC011438 Genomic DNA. Translation: AAF18258.1. Sequence problems.
    AC026875 Genomic DNA. Translation: AAF79833.1. Sequence problems.
    CP002684 Genomic DNA. Translation: AEE28251.1.
    AK117238 mRNA. Translation: BAC41914.1.
    BT005964 mRNA. Translation: AAO64899.1.
    AK222166 mRNA. Translation: BAD95276.1. Different initiation.
    PIRiS71278.
    RefSeqiNP_172293.2. NM_100689.4. [Q42572-1]
    UniGeneiAt.36.

    Genome annotation databases

    EnsemblPlantsiAT1G08130.1; AT1G08130.1; AT1G08130. [Q42572-1]
    GeneIDi837333.
    KEGGiath:AT1G08130.

    Keywords - Coding sequence diversityi

    Alternative initiation

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X97924 mRNA. Translation: CAA66599.1 .
    AC011438 Genomic DNA. Translation: AAF18258.1 . Sequence problems.
    AC026875 Genomic DNA. Translation: AAF79833.1 . Sequence problems.
    CP002684 Genomic DNA. Translation: AEE28251.1 .
    AK117238 mRNA. Translation: BAC41914.1 .
    BT005964 mRNA. Translation: AAO64899.1 .
    AK222166 mRNA. Translation: BAD95276.1 . Different initiation.
    PIRi S71278.
    RefSeqi NP_172293.2. NM_100689.4. [Q42572-1 ]
    UniGenei At.36.

    3D structure databases

    ProteinModelPortali Q42572.
    SMRi Q42572. Positions 159-776.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    STRINGi 3702.AT1G08130.1-P.

    Proteomic databases

    PaxDbi Q42572.
    PRIDEi Q42572.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblPlantsi AT1G08130.1 ; AT1G08130.1 ; AT1G08130 . [Q42572-1 ]
    GeneIDi 837333.
    KEGGi ath:AT1G08130.

    Organism-specific databases

    TAIRi AT1G08130.

    Phylogenomic databases

    eggNOGi COG1793.
    HOGENOMi HOG000036006.
    InParanoidi Q42572.
    KOi K10747.
    OMAi MVKMLEG.
    PhylomeDBi Q42572.

    Enzyme and pathway databases

    BioCyci ARA:AT1G08130-MONOMER.

    Miscellaneous databases

    PROi Q42572.

    Gene expression databases

    Genevestigatori Q42572.

    Family and domain databases

    Gene3Di 1.10.3260.10. 1 hit.
    2.40.50.140. 1 hit.
    InterProi IPR000977. DNA_ligase_ATP-dep.
    IPR012309. DNA_ligase_ATP-dep_C.
    IPR012310. DNA_ligase_ATP-dep_cent.
    IPR016059. DNA_ligase_ATP-dep_CS.
    IPR012308. DNA_ligase_ATP-dep_N.
    IPR012340. NA-bd_OB-fold.
    [Graphical view ]
    Pfami PF04679. DNA_ligase_A_C. 1 hit.
    PF01068. DNA_ligase_A_M. 1 hit.
    PF04675. DNA_ligase_A_N. 1 hit.
    [Graphical view ]
    SUPFAMi SSF117018. SSF117018. 1 hit.
    SSF50249. SSF50249. 1 hit.
    TIGRFAMsi TIGR00574. dnl1. 1 hit.
    PROSITEi PS00697. DNA_LIGASE_A1. 1 hit.
    PS00333. DNA_LIGASE_A2. 1 hit.
    PS50160. DNA_LIGASE_A3. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Molecular cloning and functional analysis of the Arabidopsis thaliana DNA ligase I homologue."
      Taylor R.M., Hamer M.J., Rosamond J., Bray C.M.
      Plant J. 14:75-81(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA].
      Strain: cv. Landsberg erecta.
    2. "Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana."
      Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K.
      , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W.
      Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: cv. Columbia.
    3. The Arabidopsis Information Resource (TAIR)
      Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
      Cited for: GENOME REANNOTATION.
      Strain: cv. Columbia.
    4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
      Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
      , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
      Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Strain: cv. Columbia.
    6. "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs."
      Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.
      , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K.
      Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 427-790.
      Strain: cv. Columbia.
    7. "An evolutionarily conserved translation initiation mechanism regulates nuclear or mitochondrial targeting of DNA ligase 1 in Arabidopsis thaliana."
      Sunderland P.A., West C.E., Waterworth W.M., Bray C.M.
      Plant J. 47:356-367(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION OF ISOFORMS 1; 2 AND 3, SUBCELLULAR LOCATION.
      Strain: cv. Columbia.
    8. "Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice."
      Shultz R.W., Tatineni V.M., Hanley-Bowdoin L., Thompson W.F.
      Plant Physiol. 144:1697-1714(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.
    9. "DNA ligase 1 deficient plants display severe growth defects and delayed repair of both DNA single and double strand breaks."
      Waterworth W.M., Kozak J., Provost C.M., Bray C.M., Angelis K.J., West C.E.
      BMC Plant Biol. 9:79-79(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, DISRUPTION PHENOTYPE.
      Strain: cv. Columbia.
    10. "DNA LIGASE I exerts a maternal effect on seed development in Arabidopsis thaliana."
      Andreuzza S., Li J., Guitton A.-E., Faure J.-E., Casanova S., Park J.-S., Choi Y., Chen Z., Berger F.
      Development 137:73-81(2010) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE.

    Entry informationi

    Entry nameiDNLI1_ARATH
    AccessioniPrimary (citable) accession number: Q42572
    Secondary accession number(s): Q541Y6
    , Q56W81, Q9LMZ4, Q9SGE5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: January 10, 2003
    Last modified: October 1, 2014
    This is version 113 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Arabidopsis thaliana
      Arabidopsis thaliana: entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3