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Protein

DNA ligase 4

Gene

LIG4

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair. May be involved for T-DNA integration even if not absolutely required. Seems to be dispensable under normal growth conditions.2 Publications

Catalytic activityi

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

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei251 – 2511ATPBy similarity
Active sitei253 – 2531N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei258 – 2581ATPBy similarity
Binding sitei273 – 2731ATPBy similarity
Metal bindingi303 – 3031Magnesium 1Sequence analysis
Metal bindingi418 – 4181Magnesium 2Sequence analysis
Binding sitei423 – 4231ATPBy similarity
Binding sitei434 – 4341ATPBy similarity
Binding sitei440 – 4401ATPBy similarity

GO - Molecular functioni

GO - Biological processi

  • cellular response to DNA damage stimulus Source: TAIR
  • DNA biosynthetic process Source: InterPro
  • DNA ligation involved in DNA repair Source: GO_Central
  • DNA recombination Source: UniProtKB-KW
  • double-strand break repair Source: TAIR
  • double-strand break repair via nonhomologous end joining Source: TAIR
  • lagging strand elongation Source: GO_Central
  • response to X-ray Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair, DNA replication

Keywords - Ligandi

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

Enzyme and pathway databases

BioCyciARA:AT5G57160-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 4 (EC:6.5.1.1)
Alternative name(s):
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4
Gene namesi
Name:LIG4
Ordered Locus Names:At5g57160
ORF Names:MUL3.11
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

TAIRiAT5G57160.

Subcellular locationi

GO - Cellular componenti

  • apoplast Source: TAIR
  • cytoplasm Source: GO_Central
  • nucleus Source: UniProtKB-SubCell
  • plasmodesma Source: TAIR
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 12191219DNA ligase 4PRO_0000059580Add
BLAST

Proteomic databases

PaxDbiQ9LL84.
PRIDEiQ9LL84.

PTM databases

iPTMnetiQ9LL84.

Expressioni

Tissue specificityi

Widely expressed, with higher levels in young flowers and roots.1 Publication

Inductioni

Induced by gamma radiation and by white light, but not by UV-B. Regulated by ATM in response to DNA double strand breaks (DSBs).2 Publications

Gene expression databases

GenevisibleiQ9LL84. AT.

Interactioni

Subunit structurei

Interacts with XRCC4 via its tandem BRCT domains.1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
XRCC4Q682V02EBI-2127971,EBI-2128002

Protein-protein interaction databases

BioGridi21066. 3 interactions.
IntActiQ9LL84. 1 interaction.
MINTiMINT-8071190.
STRINGi3702.AT5G57160.1.

Structurei

3D structure databases

ProteinModelPortaliQ9LL84.
SMRiQ9LL84. Positions 1-599, 679-909.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini651 – 73989BRCT 1PROSITE-ProRule annotationAdd
BLAST
Domaini807 – 909103BRCT 2PROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated
Contains 2 BRCT domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0966. Eukaryota.
COG1793. LUCA.
HOGENOMiHOG000083793.
InParanoidiQ9LL84.
KOiK10777.
OMAiIGEDHSR.
PhylomeDBiQ9LL84.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
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]
PfamiPF16589. BRCT_2. 1 hit.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 2 hits.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9LL84-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MTEEIKFSVL VSLFNWIQKS KTSSQKRSKF RKFLDTYCKP SDYFVAVRLI
60 70 80 90 100
IPSLDRERGS YGLKESVLAT CLIDALGISR DAPDAVRLLN WRKGGTAKAG
110 120 130 140 150
ANAGNFSLIA AEVLQRRQGM ASGGLTIKEL NDLLDRLASS ENRAEKTLVL
160 170 180 190 200
STLIQKTNAQ EMKWVIRIIL KDLKLGMSEK SIFQEFHPDA EDLFNVTCDL
210 220 230 240 250
KLVCEKLRDR HQRHKRQDIE VGKAVRPQLA MRIGDVNAAW KKLHGKDVVA
260 270 280 290 300
ECKFDGDRIQ IHKNGTDIHY FSRNFLDHSE YAHAMSDLIV QNILVDKCIL
310 320 330 340 350
DGEMLVWDTS LNRFAEFGSN QEIAKAAREG LDSHKQLCYV AFDVLYVGDT
360 370 380 390 400
SVIHQSLKER HELLKKVVKP LKGRLEVLVP EGGLNVHRPS GEPSWSIVVH
410 420 430 440 450
AAADVERFFK ETVENRDEGI VLKDLESKWE PGDRSGKWMK LKPEYIRAGA
460 470 480 490 500
DLDVLIIGGY YGSGRRGGEV AQFLVALADR AEANVYPRRF MSFCRVGTGL
510 520 530 540 550
SDDELNTVVS KLKPYFRKNE HPKKAPPSFY QVTNHSKERP DVWIDSPEKS
560 570 580 590 600
IILSITSDIR TIRSEVFVAP YSLRFPRIDK VRYDKPWHEC LDVQAFVELV
610 620 630 640 650
NSSNGTTQKQ KESESTQDNP KVNKSSKRGE KKNVSLVPSQ FIQTDVSDIK
660 670 680 690 700
GKTSIFSNMI FYFVNVPRSH SLETFHKMVV ENGGKFSMNL NNSVTHCIAA
710 720 730 740 750
ESSGIKYQAA KRQRDVIHFS WVLDCCSRNK MLPLLPKYFL HLTDASRTKL
760 770 780 790 800
QDDIDEFSDS YYWDLDLEGL KQVLSNAKQS EDSKSIDYYK KKLCPEKRWS
810 820 830 840 850
CLLSCCVYFY PYSQTLSTEE EALLGIMAKR LMLEVLMAGG KVSNNLAHAS
860 870 880 890 900
HLVVLAMAEE PLDFTLVSKS FSEMEKRLLL KKRLHVVSSH WLEESLQREE
910 920 930 940 950
KLCEDVYTLR PKYMEESDTE ESDKSEHDTT EVASQGSAQT KEPASSKIAI
960 970 980 990 1000
TSSRGRSNTR AVKRGRSSTN SLQRVQRRRG KQPSKISGDE TEESDASEEK
1010 1020 1030 1040 1050
VSTRLSDIAE ETDSFGEAQR NSSRGKCAKR GKSRVGQTQR VQRSRRGKKA
1060 1070 1080 1090 1100
AKIGGDESDE NDELDGNNNV SADAEEGNAA GRSVENEETR EPDIAKYTES
1110 1120 1130 1140 1150
QQRDNTVAVE EALQDSRNAK TEMDMKEKLQ IHEDPLQAML MKMFPIPSQK
1160 1170 1180 1190 1200
TTETSNRTTG EYRKANVSGE CESSEKRKLD AETDNTSVNA GAESDVVPPL
1210
VKKKKVSYRD VAGELLKDW
Length:1,219
Mass (Da):137,851
Last modified:October 1, 2000 - v1
Checksum:i97825B4B795E45FB
GO

Sequence cautioni

The sequence BAA97366.1 differs from that shown. Reason: Erroneous gene model prediction. Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF233527 mRNA. Translation: AAF91284.1.
AB023042 Genomic DNA. Translation: BAA97366.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED96857.1.
RefSeqiNP_568851.2. NM_125098.3.
UniGeneiAt.49182.
At.69713.

Genome annotation databases

EnsemblPlantsiAT5G57160.1; AT5G57160.1; AT5G57160.
GeneIDi835822.
GrameneiAT5G57160.1; AT5G57160.1; AT5G57160.
KEGGiath:AT5G57160.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF233527 mRNA. Translation: AAF91284.1.
AB023042 Genomic DNA. Translation: BAA97366.1. Sequence problems.
CP002688 Genomic DNA. Translation: AED96857.1.
RefSeqiNP_568851.2. NM_125098.3.
UniGeneiAt.49182.
At.69713.

3D structure databases

ProteinModelPortaliQ9LL84.
SMRiQ9LL84. Positions 1-599, 679-909.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi21066. 3 interactions.
IntActiQ9LL84. 1 interaction.
MINTiMINT-8071190.
STRINGi3702.AT5G57160.1.

PTM databases

iPTMnetiQ9LL84.

Proteomic databases

PaxDbiQ9LL84.
PRIDEiQ9LL84.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiAT5G57160.1; AT5G57160.1; AT5G57160.
GeneIDi835822.
GrameneiAT5G57160.1; AT5G57160.1; AT5G57160.
KEGGiath:AT5G57160.

Organism-specific databases

TAIRiAT5G57160.

Phylogenomic databases

eggNOGiKOG0966. Eukaryota.
COG1793. LUCA.
HOGENOMiHOG000083793.
InParanoidiQ9LL84.
KOiK10777.
OMAiIGEDHSR.
PhylomeDBiQ9LL84.

Enzyme and pathway databases

BioCyciARA:AT5G57160-MONOMER.

Miscellaneous databases

PROiQ9LL84.

Gene expression databases

GenevisibleiQ9LL84. AT.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
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]
PfamiPF16589. BRCT_2. 1 hit.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 2 hits.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Arabidopsis DNA ligase IV is induced by gamma-irradiation and interacts with an Arabidopsis homologue of the double strand break repair protein XRCC4."
    West C.E., Waterworth W.M., Jiang Q., Bray C.M.
    Plant J. 24:67-78(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA], INDUCTION, TISSUE SPECIFICITY, INTERACTION WITH XRCC4.
  2. "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones."
    Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H., Tabata S.
    DNA Res. 7:31-63(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  3. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  4. "The Arabidopsis AtLIG4 gene is required for the repair of DNA damage, but not for the integration of Agrobacterium T-DNA."
    van Attikum H., Bundock P., Overmeer R.M., Lee L.-Y., Gelvin S.B., Hooykaas P.J.J.
    Nucleic Acids Res. 31:4247-4255(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "AtATM is essential for meiosis and the somatic response to DNA damage in plants."
    Garcia V., Bruchet H., Camescasse D., Granier F., Bouchez D., Tissier A.
    Plant Cell 15:119-132(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: INDUCTION.
  6. "Ku80- and DNA ligase IV-deficient plants are sensitive to ionizing radiation and defective in T-DNA integration."
    Friesner J., Britt A.B.
    Plant J. 34:427-440(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiDNLI4_ARATH
AccessioniPrimary (citable) accession number: Q9LL84
Secondary accession number(s): Q9LU70
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 24, 2006
Last sequence update: October 1, 2000
Last modified: May 11, 2016
This is version 113 of the entry and version 1 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.