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Protein

DNA ligase 1

Gene

LIG1

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionLigase
Biological processCell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication
LigandATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

ReactomeiR-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

AraportiAT1G08130
TAIRilocus:2199953 AT1G08130

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

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

ExpressionAtlasiQ42572 baseline and differential
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
OMAiWIKYKRD
OrthoDBiEOG0936033M
PhylomeDBiQ42572

Family and domain databases

Gene3Di1.10.3260.10, 1 hit
InterProiView protein in InterPro
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
IPR036599 DNA_ligase_N_sf
IPR012340 NA-bd_OB-fold
PfamiView protein in Pfam
PF04679 DNA_ligase_A_C, 1 hit
PF01068 DNA_ligase_A_M, 1 hit
PF04675 DNA_ligase_A_N, 1 hit
SUPFAMiSSF117018 SSF117018, 1 hit
SSF50249 SSF50249, 1 hit
TIGRFAMsiTIGR00574 dnl1, 1 hit
PROSITEiView protein in PROSITE
PS00697 DNA_LIGASE_A1, 1 hit
PS00333 DNA_LIGASE_A2, 1 hit
PS50160 DNA_LIGASE_A3, 1 hit

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 [Q42572-1]
KEGGiath:AT1G08130

Keywords - Coding sequence diversityi

Alternative initiation

Similar proteinsi

Entry informationi

Entry nameiDNLI1_ARATH
AccessioniPrimary (citable) accession number: Q42572
Secondary accession number(s): Q541Y6
, Q56W81, Q9LMZ4, Q9SGE5
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 10, 2003
Last modified: April 25, 2018
This is version 141 of the entry and version 2 of the sequence. See 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
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