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Q42572

- DNLI1_ARATH

UniProt

Q42572 - DNLI1_ARATH

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Protein
DNA ligase 1
Gene
LIG1, At1g08130, T23G18.1, T6D22.23
Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at transcript leveli

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).

Cofactori

Magnesium By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sitei193 – 1931Interaction with target DNA By similarity
Binding sitei442 – 4421ATP By similarity
Active sitei444 – 4441N6-AMP-lysine intermediate By similarity
Binding sitei449 – 4491ATP By similarity
Binding sitei465 – 4651ATP By similarity
Sitei466 – 4661Interaction with target DNA By similarity
Metal bindingi497 – 4971Magnesium 1 By similarity
Metal bindingi596 – 5961Magnesium 2 By similarity
Binding sitei601 – 6011ATP By similarity
Binding sitei614 – 6141ATP By similarity
Binding sitei620 – 6201ATP By similarity
Sitei646 – 6461Interaction with target DNA By similarity
Sitei671 – 6711Interaction with target DNA By 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. DNA ligation Source: RefGenome
  2. DNA ligation involved in DNA repair Source: InterPro
  3. DNA recombination Source: UniProtKB-KW
  4. DNA replication Source: UniProtKB
  5. cell cycle Source: UniProtKB-KW
  6. cell division Source: UniProtKB-KW
  7. double-strand break repair Source: UniProtKB
  8. single strand break repair Source: UniProtKB
Complete GO annotation...

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

Isoform 1 : Mitochondrion 2 Publications
Isoform 2 : Nucleus 2 Publications
Isoform 3 : Nucleus 2 Publications

GO - Cellular componenti

  1. mitochondrion Source: TAIR
  2. nucleus Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

Pathology & Biotechi

Disruption phenotypei

Lethal.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transit peptidei1 – 6464Mitochondrion Reviewed prediction
Add
BLAST
Chaini65 – 790726DNA ligase 1
PRO_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.

Family & Domainsi

Region

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

Motif

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

Sequence similaritiesi

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.

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 5959Missing in isoform 3.
VSP_043693Add
BLAST
Alternative sequencei1 – 4747Missing in isoform 2.
VSP_043694Add
BLAST

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti639 – 6391A → P in CAA66599. 1 Publication

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

« Hide 'large scale' publications
  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: May 14, 2014
This is version 112 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

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