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Q42572 (DNLI1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 112. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (2) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA ligase 1

Short name=AtLIG1
EC=6.5.1.1
Alternative name(s):
DNA ligase I
Polydeoxyribonucleotide synthase [ATP] 1
Gene names
Name:LIG1
Ordered Locus Names:At1g08130
ORF Names:T23G18.1, T6D22.23
OrganismArabidopsis thaliana (Mouse-ear cress) [Reference proteome]
Taxonomic identifier3702 [NCBI]
Taxonomic lineageEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis

Protein attributes

Sequence length790 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

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. Ref.9 Ref.10

Catalytic activity

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).

Cofactor

Magnesium By similarity.

Subcellular location

Isoform 1: Mitochondrion Ref.7 Ref.10.

Isoform 2: Nucleus Ref.7 Ref.10.

Isoform 3: Nucleus Ref.7 Ref.10.

Tissue specificity

Expressed in all vegetative and reproductive tissues. Ref.10

Developmental stage

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. Ref.10

Disruption phenotype

Lethal. Ref.9

Sequence similarities

Belongs to the ATP-dependent DNA ligase family.

Sequence caution

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.

The sequence BAD95276.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
   Biological processCell cycle
Cell division
DNA damage
DNA recombination
DNA repair
DNA replication
   Cellular componentMitochondrion
Nucleus
   Coding sequence diversityAlternative initiation
   DomainRepeat
Transit peptide
   LigandATP-binding
Magnesium
Metal-binding
Nucleotide-binding
   Molecular functionLigase
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processDNA ligation

Inferred from Biological aspect of Ancestor. Source: RefGenome

DNA ligation involved in DNA repair

Inferred from electronic annotation. Source: InterPro

DNA recombination

Inferred from electronic annotation. Source: UniProtKB-KW

DNA replication

Inferred from mutant phenotype Ref.9. Source: UniProtKB

cell cycle

Inferred from electronic annotation. Source: UniProtKB-KW

cell division

Inferred from electronic annotation. Source: UniProtKB-KW

double-strand break repair

Inferred from mutant phenotype Ref.9. Source: UniProtKB

single strand break repair

Inferred from mutant phenotype Ref.9. Source: UniProtKB

   Cellular_componentmitochondrion

Inferred from direct assay Ref.7. Source: TAIR

nucleus

Inferred from direct assay Ref.7. Source: TAIR

   Molecular_functionATP binding

Inferred from electronic annotation. Source: UniProtKB-KW

DNA binding

Inferred from electronic annotation. Source: InterPro

DNA ligase (ATP) activity

Inferred from Biological aspect of Ancestor. Source: RefGenome

metal ion binding

Inferred from electronic annotation. Source: UniProtKB-KW

Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative initiation. [Align] [Select]
Isoform 1 (identifier: Q42572-1)

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.
Isoform 2 (identifier: Q42572-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-47: Missing.
Isoform 3 (identifier: Q42572-3)

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

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Transit peptide1 – 6464Mitochondrion Potential
Chain65 – 790726DNA ligase 1
PRO_0000059586

Regions

Region337 – 34610Interaction with target DNA By similarity
Region518 – 5203Interaction with target DNA By similarity
Motif68 – 758Nuclear localization signal 1 By similarity
Motif505 – 5128Nuclear localization signal 2 By similarity

Sites

Active site4441N6-AMP-lysine intermediate By similarity
Metal binding4971Magnesium 1 By similarity
Metal binding5961Magnesium 2 By similarity
Binding site4421ATP By similarity
Binding site4491ATP By similarity
Binding site4651ATP By similarity
Binding site6011ATP By similarity
Binding site6141ATP By similarity
Binding site6201ATP By similarity
Site1931Interaction with target DNA By similarity
Site4661Interaction with target DNA By similarity
Site6461Interaction with target DNA By similarity
Site6711Interaction with target DNA By similarity

Natural variations

Alternative sequence1 – 5959Missing in isoform 3.
VSP_043693
Alternative sequence1 – 4747Missing in isoform 2.
VSP_043694

Experimental info

Sequence conflict6391A → P in CAA66599. Ref.1

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified January 10, 2003. Version 2.
Checksum: 674EB9CAA9C5D329

FASTA79087,740
        10         20         30         40         50         60 
MLAIRSSNYL RCIPSLCTKT QISQFSSVLI SFSRQISHLR LSSCHRAMSS SRPSAFDALM 

        70         80         90        100        110        120 
SNARAAAKKK TPQTTNLSRS PNKRKIGETQ DANLGKTIVS EGTLPKTEDL LEPVSDSANP 

       130        140        150        160        170        180 
RSDTSSIAED SKTGAKKAKT LSKTDEMKSK IGLLKKKPND FDPEKMSCWE KGERVPFLFV 

       190        200        210        220        230        240 
ALAFDLISNE SGRIVITDIL CNMLRTVIAT TPEDLVATVY LSANEIAPAH EGVELGIGES 

       250        260        270        280        290        300 
TIIKAISEAF GRTEDHVKKQ NTELGDLGLV AKGSRSTQTM MFKPEPLTVV KVFDTFRQIA 

       310        320        330        340        350        360 
KESGKDSNEK KKNRMKALLV ATTDCEPLYL TRLLQAKLRL GFSGQTVLAA LGQAAVYNEE 

       370        380        390        400        410        420 
HSKPPPNTKS PLEEAAKIVK QVFTVLPVYD IIVPALLSGG VWNLPKTCNF TLGVPIGPML 

       430        440        450        460        470        480 
AKPTKGVAEI LNKFQDIVFT CEYKYDGERA QIHFMEDGTF EIYSRNAERN TGKYPDVALA 

       490        500        510        520        530        540 
LSRLKKPSVK SFILDCEVVA FDREKKKILP FQILSTRARK NVNVNDIKVG VCIFAFDMLY 

       550        560        570        580        590        600 
LNGQQLIQEN LKIRREKLYE SFEEDPGYFQ FATAVTSNDI DEIQKFLDAS VDVGCEGLII 

       610        620        630        640        650        660 
KTLDSDATYE PAKRSNNWLK LKKDYMDSIG DSVDLVPIAA FHGRGKRTGV YGAFLLACYD 

       670        680        690        700        710        720 
VDKEEFQSIC KIGTGFSDAM LDERSSSLRS QVIATPKQYY RVGDSLNPDV WFEPTEVWEV 

       730        740        750        760        770        780 
KAADLTISPV HRAATGIVDP DKGISLRFPR LLRVREDKKP EEATSSEQIA DLYQAQKHNH 

       790 
PSNEVKGDDD 

« Hide

Isoform 2 [UniParc].

Checksum: D7DCE08F0DBC0C4D
Show »

FASTA74382,417
Isoform 3 [UniParc].

Checksum: 72E76F2F2A57830B
Show »

FASTA73181,167

References

« Hide 'large scale' references
[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. expand/collapse author list , 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]"Functional annotation of a full-length Arabidopsis cDNA collection."
Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A., Shinozaki K.
Science 296:141-145(2002) [PubMed] [Europe PMC] [Abstract]
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. expand/collapse author list , 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. expand/collapse author list , 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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRS71278.
RefSeqNP_172293.2. NM_100689.4. [Q42572-1]
UniGeneAt.36.

3D structure databases

ProteinModelPortalQ42572.
SMRQ42572. Positions 159-776.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING3702.AT1G08130.1-P.

Proteomic databases

PaxDbQ42572.
PRIDEQ42572.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsAT1G08130.1; AT1G08130.1; AT1G08130. [Q42572-1]
GeneID837333.
KEGGath:AT1G08130.

Organism-specific databases

TAIRAT1G08130.

Phylogenomic databases

eggNOGCOG1793.
HOGENOMHOG000036006.
InParanoidQ42572.
KOK10747.
OMAMVKMLEG.
PhylomeDBQ42572.

Enzyme and pathway databases

BioCycARA:AT1G08130-MONOMER.

Gene expression databases

GenevestigatorQ42572.

Family and domain databases

Gene3D1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
InterProIPR000977. 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]
PfamPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SUPFAMSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
TIGRFAMsTIGR00574. dnl1. 1 hit.
PROSITEPS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

PROQ42572.

Entry information

Entry nameDNLI1_ARATH
AccessionPrimary (citable) accession number: Q42572
Secondary accession number(s): Q541Y6 expand/collapse secondary AC list , Q56W81, Q9LMZ4, Q9SGE5
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

Arabidopsis thaliana

Arabidopsis thaliana: entries and gene names