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Protein

DNA ligase 4

Gene

Lig4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at transcript 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 and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends (By similarity).By similarity

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 sitei271 – 2711ATPBy similarity
Active sitei273 – 2731N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei278 – 2781ATPBy similarity
Binding sitei293 – 2931ATPBy similarity
Metal bindingi331 – 3311Magnesium 1Sequence Analysis
Metal bindingi427 – 4271Magnesium 2Sequence Analysis
Binding sitei432 – 4321ATPBy similarity
Binding sitei443 – 4431ATPBy similarity
Binding sitei449 – 4491ATPBy similarity

GO - Molecular functioni

  1. ATP binding Source: MGI
  2. DNA binding Source: MGI
  3. DNA ligase (ATP) activity Source: MGI
  4. DNA ligase activity Source: MGI
  5. ligase activity Source: MGI
  6. metal ion binding Source: UniProtKB-KW
  7. protein C-terminus binding Source: MGI

GO - Biological processi

  1. cell cycle Source: UniProtKB-KW
  2. cell division Source: UniProtKB-KW
  3. cell proliferation Source: MGI
  4. cellular response to lithium ion Source: Ensembl
  5. central nervous system development Source: MGI
  6. chromosome organization Source: MGI
  7. DNA biosynthetic process Source: InterPro
  8. DNA ligation Source: MGI
  9. DNA ligation involved in DNA recombination Source: MGI
  10. DNA ligation involved in DNA repair Source: MGI
  11. DNA repair Source: MGI
  12. double-strand break repair Source: MGI
  13. double-strand break repair via nonhomologous end joining Source: MGI
  14. immunoglobulin V(D)J recombination Source: MGI
  15. in utero embryonic development Source: MGI
  16. isotype switching Source: MGI
  17. lagging strand elongation Source: GO_Central
  18. negative regulation of neuron apoptotic process Source: MGI
  19. neuron apoptotic process Source: MGI
  20. nucleotide-excision repair Source: GO_Central
  21. nucleotide-excision repair, DNA gap filling Source: MGI
  22. positive regulation of fibroblast proliferation Source: MGI
  23. positive regulation of neurogenesis Source: MGI
  24. pro-B cell differentiation Source: MGI
  25. response to gamma radiation Source: MGI
  26. response to ionizing radiation Source: MGI
  27. response to X-ray Source: MGI
  28. single strand break repair Source: MGI
  29. somatic stem cell maintenance Source: MGI
  30. T cell differentiation in thymus Source: MGI
  31. T cell receptor V(D)J recombination Source: MGI
  32. V(D)J recombination Source: MGI
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

ReactomeiREACT_254501. Nonhomologous End-joining (NHEJ).

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
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 8

Organism-specific databases

MGIiMGI:1335098. Lig4.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. chromosome Source: GO_Central
  2. condensed chromosome Source: MGI
  3. cytoplasm Source: MGI
  4. DNA-dependent protein kinase-DNA ligase 4 complex Source: MGI
  5. DNA ligase IV complex Source: MGI
  6. focal adhesion Source: MGI
  7. nonhomologous end joining complex Source: UniProtKB
  8. nucleoplasm Source: MGI
  9. nucleus Source: MGI
  10. plasma membrane Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 911911DNA ligase 4PRO_0000059577Add
BLAST

Proteomic databases

MaxQBiQ8BTF7.
PaxDbiQ8BTF7.
PRIDEiQ8BTF7.

PTM databases

PhosphoSiteiQ8BTF7.

Expressioni

Gene expression databases

CleanExiMM_LIG4.
GenevestigatoriQ8BTF7.

Interactioni

Subunit structurei

Binds to XRCC4. The LIG4-XRCC4 complex has probably a 1:2 stoichiometry. The LIG4-XRCC4 heteromer associates in a DNA-dependent manner with the DNA-dependent protein kinase complex DNA-PK, formed by the Ku p70/p86 dimer (G22P1/G22P2) and PRKDC. Interacts with APLF (By similarity).By similarity

Structurei

3D structure databases

ProteinModelPortaliQ8BTF7.
SMRiQ8BTF7. Positions 6-605, 654-911.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini654 – 74390BRCT 1PROSITE-ProRule annotationAdd
BLAST
Domaini808 – 911104BRCT 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

eggNOGiCOG1793.
GeneTreeiENSGT00780000122044.
HOGENOMiHOG000007831.
HOVERGENiHBG005516.
InParanoidiQ8BTF7.
KOiK10777.
OMAiLQEENQY.
OrthoDBiEOG7BKCT2.
TreeFamiTF312980.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.40.50.10190. 2 hits.
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.
IPR021536. DNA_ligase_IV_dom.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
PfamiPF00533. BRCT. 2 hits.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
PF11411. DNA_ligase_IV. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 2 hits.
[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.

Q8BTF7-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASSQTSQTV AAHVPFADLC STLERIQKGK DRAEKIRHFK EFLDSWRKFH
60 70 80 90 100
DALHKNRKDV TDSFYPAMRL ILPQLERERM AYGIKETMLA KLYIELLNLP
110 120 130 140 150
REGKDAQKLL NYRTPSGART DAGDFAMIAY FVLKPRCLQK GSLTIQQVNE
160 170 180 190 200
LLDLVASNNS GKKKDLVKKS LLQLITQSSA LEQKWLIRMI IKDLKLGISQ
210 220 230 240 250
QTIFSIFHND AVELHNVTTD LEKVCRQLHD PSVGLSDISI TLFSAFKPML
260 270 280 290 300
AAVADVERVE KDMKQQSFYI ETKLDGERMQ MHKDGALYRY FSRNGYNYTD
310 320 330 340 350
QFGESPQEGS LTPFIHNAFG TDVQACILDG EMMAYNPTTQ TFMQKGVKFD
360 370 380 390 400
IKRMVEDSGL QTCYSVFDVL MVNKKKLGRE TLRKRYEILS STFTPIQGRI
410 420 430 440 450
EIVQKTQAHT KKEVVDALND AIDKREEGIM VKHPLSIYKP DKRGEGWLKI
460 470 480 490 500
KPEYVSGLMD ELDVLIVGGY WGKGSRGGMM SHFLCAVAET PPPGDRPSVF
510 520 530 540 550
HTLCRVGSGY TMKELYDLGL KLAKYWKPFH KKSPPSSILC GTEKPEVYIE
560 570 580 590 600
PQNSVIVQIK AAEIVPSDMY KTGSTLRFPR IEKIRDDKEW HECMTLGDLE
610 620 630 640 650
QLRGKASGKL ATKHLHVGDD DEPREKRRKP ISKTKKAIRI IEHLKAPNLS
660 670 680 690 700
NVNKVSNVFE DVEFCVMSGL DGYPKADLEN RIAEFGGYIV QNPGPDTYCV
710 720 730 740 750
IAGSENVRVK NIISSDKNDV VKPEWLLECF KTKTCVPWQP RFMIHMCPST
760 770 780 790 800
KQHFAREYDC YGDSYFVDTD LDQLKEVFLG IKPSEQQTPE EMAPVIADLE
810 820 830 840 850
CRYSWDHSPL SMFRHYTIYL DLYAVINDLS SRIEATRLGI TALELRFHGA
860 870 880 890 900
KVVSCLSEGV SHVIIGEDQR RVTDFKIFRR MLKKKFKILQ ESWVSDSVDK
910
GELQEENQYL L
Length:911
Mass (Da):104,120
Last modified:October 3, 2012 - v2
Checksum:i20CDD0F6465355A2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti268 – 2681F → L in BAC26747 (PubMed:16141072).Curated
Sequence conflicti758 – 7581Y → C in BAE28333 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK030029 mRNA. Translation: BAC26747.1.
AK148081 mRNA. Translation: BAE28333.1.
AC138397 Genomic DNA. No translation available.
CH466566 Genomic DNA. Translation: EDL22038.1.
CH466566 Genomic DNA. Translation: EDL22040.1.
CCDSiCCDS22092.1.
RefSeqiNP_795927.2. NM_176953.3.
UniGeneiMm.80584.

Genome annotation databases

EnsembliENSMUST00000095476; ENSMUSP00000093130; ENSMUSG00000049717.
ENSMUST00000170033; ENSMUSP00000130807; ENSMUSG00000049717.
GeneIDi319583.
KEGGimmu:319583.
UCSCiuc009kul.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK030029 mRNA. Translation: BAC26747.1.
AK148081 mRNA. Translation: BAE28333.1.
AC138397 Genomic DNA. No translation available.
CH466566 Genomic DNA. Translation: EDL22038.1.
CH466566 Genomic DNA. Translation: EDL22040.1.
CCDSiCCDS22092.1.
RefSeqiNP_795927.2. NM_176953.3.
UniGeneiMm.80584.

3D structure databases

ProteinModelPortaliQ8BTF7.
SMRiQ8BTF7. Positions 6-605, 654-911.
ModBaseiSearch...
MobiDBiSearch...

PTM databases

PhosphoSiteiQ8BTF7.

Proteomic databases

MaxQBiQ8BTF7.
PaxDbiQ8BTF7.
PRIDEiQ8BTF7.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000095476; ENSMUSP00000093130; ENSMUSG00000049717.
ENSMUST00000170033; ENSMUSP00000130807; ENSMUSG00000049717.
GeneIDi319583.
KEGGimmu:319583.
UCSCiuc009kul.1. mouse.

Organism-specific databases

CTDi3981.
MGIiMGI:1335098. Lig4.

Phylogenomic databases

eggNOGiCOG1793.
GeneTreeiENSGT00780000122044.
HOGENOMiHOG000007831.
HOVERGENiHBG005516.
InParanoidiQ8BTF7.
KOiK10777.
OMAiLQEENQY.
OrthoDBiEOG7BKCT2.
TreeFamiTF312980.

Enzyme and pathway databases

ReactomeiREACT_254501. Nonhomologous End-joining (NHEJ).

Miscellaneous databases

NextBioi395028.
PROiQ8BTF7.
SOURCEiSearch...

Gene expression databases

CleanExiMM_LIG4.
GenevestigatoriQ8BTF7.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.40.50.10190. 2 hits.
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.
IPR021536. DNA_ligase_IV_dom.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
PfamiPF00533. BRCT. 2 hits.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
PF11411. DNA_ligase_IV. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 2 hits.
[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

  1. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: C57BL/6J.
    Tissue: Testis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].

Entry informationi

Entry nameiDNLI4_MOUSE
AccessioniPrimary (citable) accession number: Q8BTF7
Secondary accession number(s): G3UWC4, Q3UG76
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: October 3, 2012
Last modified: March 4, 2015
This is version 107 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.