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Protein

DNA ligase 1

Gene

LIG1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: 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)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.PROSITE-ProRule annotation

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei442ATPBy similarity1
Active sitei444N6-AMP-lysine intermediatePROSITE-ProRule annotation1
Binding sitei449ATPBy similarity1
Binding sitei465ATPBy similarity1
Metal bindingi497Magnesium 1By similarity1
Metal bindingi596Magnesium 2By similarity1
Binding sitei601ATPBy similarity1
Binding sitei614ATPBy similarity1
Binding sitei620ATPBy similarity1

GO - Molecular functioni

GO - Biological processi

  • cell cycle Source: UniProtKB-KW
  • cell division Source: UniProtKB-KW
  • DNA biosynthetic process Source: InterPro
  • DNA demethylation Source: TAIR
  • DNA ligation involved in DNA repair Source: GO_Central
  • DNA recombination Source: UniProtKB-KW
  • DNA replication Source: UniProtKB
  • double-strand break repair Source: UniProtKB
  • lagging strand elongation Source: GO_Central
  • 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

ReactomeiR-ATH-110362. POLB-Dependent Long Patch Base Excision Repair.
R-ATH-174414. Processive synthesis on the C-strand of the telomere.
R-ATH-5358565. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
R-ATH-5358606. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
R-ATH-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-ATH-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-ATH-69183. Processive synthesis on the lagging strand.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 1 (EC:6.5.1.1PROSITE-ProRule annotation)
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
Proteomesi
  • UP000006548 Componenti: Chromosome 1

Organism-specific databases

TAIRiAT1G08130.

Subcellular locationi

GO - Cellular componenti

  • mitochondrion Source: TAIR
  • nucleolus Source: TAIR
  • 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)DescriptionActionsGraphical viewLength
Transit peptidei1 – 64MitochondrionSequence analysisAdd BLAST64
ChainiPRO_000005958665 – 790DNA ligase 1Add BLAST726

Proteomic databases

PaxDbiQ42572.
PRIDEiQ42572.

PTM databases

iPTMnetiQ42572.

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

GenevisibleiQ42572. AT.

Interactioni

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sitei193Interaction with target DNABy similarity1
Sitei466Interaction with target DNABy similarity1
Sitei646Interaction with target DNABy similarity1
Sitei671Interaction with target DNABy similarity1

Protein-protein interaction databases

STRINGi3702.AT1G08130.1.

Structurei

3D structure databases

ProteinModelPortaliQ42572.
SMRiQ42572.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni337 – 346Interaction with target DNABy similarity10
Regioni518 – 520Interaction with target DNABy similarity3

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi68 – 75Nuclear localization signal 1By similarity8
Motifi505 – 512Nuclear localization signal 2By similarity8

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated

Keywords - Domaini

Repeat, Transit peptide

Phylogenomic databases

eggNOGiKOG0967. Eukaryota.
COG1793. LUCA.
HOGENOMiHOG000036006.
InParanoidiQ42572.
KOiK10747.
OMAiSQCPNYD.
OrthoDBiEOG0936033M.
PhylomeDBiQ42572.

Family and domain databases

Gene3Di1.10.3260.10. 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. AlignAdd to basket

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

        10         20         30         40         50
MLAIRSSNYL RCIPSLCTKT QISQFSSVLI SFSRQISHLR LSSCHRAMSS
60 70 80 90 100
SRPSAFDALM SNARAAAKKK TPQTTNLSRS PNKRKIGETQ DANLGKTIVS
110 120 130 140 150
EGTLPKTEDL LEPVSDSANP RSDTSSIAED SKTGAKKAKT LSKTDEMKSK
160 170 180 190 200
IGLLKKKPND FDPEKMSCWE KGERVPFLFV ALAFDLISNE SGRIVITDIL
210 220 230 240 250
CNMLRTVIAT TPEDLVATVY LSANEIAPAH EGVELGIGES TIIKAISEAF
260 270 280 290 300
GRTEDHVKKQ NTELGDLGLV AKGSRSTQTM MFKPEPLTVV KVFDTFRQIA
310 320 330 340 350
KESGKDSNEK KKNRMKALLV ATTDCEPLYL TRLLQAKLRL GFSGQTVLAA
360 370 380 390 400
LGQAAVYNEE HSKPPPNTKS PLEEAAKIVK QVFTVLPVYD IIVPALLSGG
410 420 430 440 450
VWNLPKTCNF TLGVPIGPML AKPTKGVAEI LNKFQDIVFT CEYKYDGERA
460 470 480 490 500
QIHFMEDGTF EIYSRNAERN TGKYPDVALA LSRLKKPSVK SFILDCEVVA
510 520 530 540 550
FDREKKKILP FQILSTRARK NVNVNDIKVG VCIFAFDMLY LNGQQLIQEN
560 570 580 590 600
LKIRREKLYE SFEEDPGYFQ FATAVTSNDI DEIQKFLDAS VDVGCEGLII
610 620 630 640 650
KTLDSDATYE PAKRSNNWLK LKKDYMDSIG DSVDLVPIAA FHGRGKRTGV
660 670 680 690 700
YGAFLLACYD VDKEEFQSIC KIGTGFSDAM LDERSSSLRS QVIATPKQYY
710 720 730 740 750
RVGDSLNPDV WFEPTEVWEV KAADLTISPV HRAATGIVDP DKGISLRFPR
760 770 780 790
LLRVREDKKP EEATSSEQIA DLYQAQKHNH PSNEVKGDDD
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 AAF18258 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence AAF79833 differs from that shown. Reason: Erroneous gene model prediction.Curated
The sequence BAD95276 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti639A → P in CAA66599 (PubMed:9681027).Curated1

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0436931 – 59Missing in isoform 3. CuratedAdd BLAST59
Alternative sequenceiVSP_0436941 – 47Missing in isoform 2. CuratedAdd BLAST47

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_100689.5. [Q42572-1]
UniGeneiAt.36.

Genome annotation databases

EnsemblPlantsiAT1G08130.1; AT1G08130.1; AT1G08130. [Q42572-1]
GeneIDi837333.
GrameneiAT1G08130.1; AT1G08130.1; AT1G08130.
KEGGiath:AT1G08130.

Keywords - Coding sequence diversityi

Alternative initiation

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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_100689.5. [Q42572-1]
UniGeneiAt.36.

3D structure databases

ProteinModelPortaliQ42572.
SMRiQ42572.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi3702.AT1G08130.1.

PTM databases

iPTMnetiQ42572.

Proteomic databases

PaxDbiQ42572.
PRIDEiQ42572.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT1G08130.1; AT1G08130.1; AT1G08130. [Q42572-1]
GeneIDi837333.
GrameneiAT1G08130.1; AT1G08130.1; AT1G08130.
KEGGiath:AT1G08130.

Organism-specific databases

TAIRiAT1G08130.

Phylogenomic databases

eggNOGiKOG0967. Eukaryota.
COG1793. LUCA.
HOGENOMiHOG000036006.
InParanoidiQ42572.
KOiK10747.
OMAiSQCPNYD.
OrthoDBiEOG0936033M.
PhylomeDBiQ42572.

Enzyme and pathway databases

ReactomeiR-ATH-110362. POLB-Dependent Long Patch Base Excision Repair.
R-ATH-174414. Processive synthesis on the C-strand of the telomere.
R-ATH-5358565. Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha).
R-ATH-5358606. Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta).
R-ATH-5651801. PCNA-Dependent Long Patch Base Excision Repair.
R-ATH-6782210. Gap-filling DNA repair synthesis and ligation in TC-NER.
R-ATH-69183. Processive synthesis on the lagging strand.

Miscellaneous databases

PROiQ42572.

Gene expression databases

GenevisibleiQ42572. AT.

Family and domain databases

Gene3Di1.10.3260.10. 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]
ProtoNetiSearch...

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: November 30, 2016
This is version 131 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.