Q8BTF7 (DNLI4_MOUSE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA ligase 4
EC=6.5.1.1

Alternative name(s):
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4

Gene names

Name:

Lig4

Organism

Mus musculus (Mouse) [Reference proteome]

Taxonomic identifier

10090 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Mus › Mus

Protein attributes

Sequence length	911 AA.
Sequence status	Complete.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	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.
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Cofactor	Magnesium By similarity.
Subunit structure	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.
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the ATP-dependent DNA ligase family. Contains 2 BRCT domains.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Cellular component	Nucleus
Domain	Repeat
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA ligation involved in DNA recombination Inferred from mutant phenotype PubMed 9823897. Source: MGI DNA ligation involved in DNA repair Inferred from mutant phenotype PubMed 9823897. Source: MGI T cell differentiation in thymus Inferred from mutant phenotype PubMed 10911993PubMed 9823897. Source: MGI T cell receptor V(D)J recombination Inferred from mutant phenotype PubMed 10911993. Source: MGI cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW cell proliferation Inferred from mutant phenotype PubMed 15175260PubMed 17554302. Source: MGI cellular response to lithium ion Inferred from electronic annotation. Source: Compara central nervous system development Inferred from mutant phenotype PubMed 9875844PubMed 9889105. Source: MGI chromosome organization Inferred from genetic interaction PubMed 15175260. Source: MGI double-strand break repair via nonhomologous end joining Inferred from mutant phenotype PubMed 10823907PubMed 16777961. Source: MGI immunoglobulin V(D)J recombination Inferred from mutant phenotype PubMed 9823897. Source: MGI in utero embryonic development Inferred from mutant phenotype PubMed 10911993PubMed 16777961PubMed 9823897. Source: MGI isotype switching Inferred from mutant phenotype PubMed 17713479. Source: MGI lagging strand elongation Inferred from Biological aspect of Ancestor. Source: RefGenome negative regulation of neuron apoptotic process Inferred from mutant phenotype PubMed 9875844. Source: MGI neuron apoptotic process Inferred from genetic interaction PubMed 11248063. Source: MGI nucleotide-excision repair Inferred from Biological aspect of Ancestor. Source: RefGenome nucleotide-excision repair, DNA gap filling Inferred from electronic annotation. Source: Compara positive regulation of fibroblast proliferation Inferred from mutant phenotype PubMed 10911993PubMed 9823897. Source: MGI positive regulation of neurogenesis Inferred from mutant phenotype PubMed 10716994PubMed 16777961PubMed 9875844. Source: MGI pro-B cell differentiation Inferred from mutant phenotype PubMed 10911993PubMed 9823897. Source: MGI response to X-ray Inferred from electronic annotation. Source: Compara response to gamma radiation Inferred from mutant phenotype PubMed 10911993PubMed 9823897. Source: MGI single strand break repair Inferred from electronic annotation. Source: Compara somatic stem cell maintenance Inferred from mutant phenotype PubMed 17554302. Source: MGI
Cellular_component	DNA ligase IV complex Inferred from Biological aspect of Ancestor. Source: RefGenome DNA-dependent protein kinase-DNA ligase 4 complex Inferred from direct assay PubMed 15194694. Source: MGI chromosome Inferred from Biological aspect of Ancestor. Source: RefGenome condensed chromosome Inferred from electronic annotation. Source: Compara cytoplasm Inferred from electronic annotation. Source: Compara focal adhesion Inferred from electronic annotation. Source: Compara plasma membrane Inferred from electronic annotation. Source: Compara
Molecular_function	ATP binding Inferred from direct assay PubMed 15194694. Source: MGI DNA binding Inferred from electronic annotation. Source: Compara DNA ligase (ATP) activity Inferred from direct assay PubMed 15194694. Source: MGI metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 911	911	DNA ligase 4		PRO_0000059577
Regions
	Domain	654 – 743	90	BRCT 1
	Domain	808 – 911	104	BRCT 2
Sites
	Active site	273	1	N6-AMP-lysine intermediate By similarity
	Metal binding	331	1	Magnesium 1 Potential
	Metal binding	427	1	Magnesium 2 Potential
	Binding site	271	1	ATP By similarity
	Binding site	278	1	ATP By similarity
	Binding site	293	1	ATP By similarity
	Binding site	432	1	ATP By similarity
	Binding site	443	1	ATP By similarity
	Binding site	449	1	ATP By similarity
Experimental info
	Sequence conflict	268	1	F → L in BAC26747. Ref.1
	Sequence conflict	758	1	Y → C in BAE28333. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Q8BTF7 [UniParc]. Last modified October 3, 2012. Version 2. Checksum: 20CDD0F6465355A2	FASTA	911	104,120
	10 20 30 40 50 60 MASSQTSQTV AAHVPFADLC STLERIQKGK DRAEKIRHFK EFLDSWRKFH DALHKNRKDV 70 80 90 100 110 120 TDSFYPAMRL ILPQLERERM AYGIKETMLA KLYIELLNLP REGKDAQKLL NYRTPSGART 130 140 150 160 170 180 DAGDFAMIAY FVLKPRCLQK GSLTIQQVNE LLDLVASNNS GKKKDLVKKS LLQLITQSSA 190 200 210 220 230 240 LEQKWLIRMI IKDLKLGISQ QTIFSIFHND AVELHNVTTD LEKVCRQLHD PSVGLSDISI 250 260 270 280 290 300 TLFSAFKPML AAVADVERVE KDMKQQSFYI ETKLDGERMQ MHKDGALYRY FSRNGYNYTD 310 320 330 340 350 360 QFGESPQEGS LTPFIHNAFG TDVQACILDG EMMAYNPTTQ TFMQKGVKFD IKRMVEDSGL 370 380 390 400 410 420 QTCYSVFDVL MVNKKKLGRE TLRKRYEILS STFTPIQGRI EIVQKTQAHT KKEVVDALND 430 440 450 460 470 480 AIDKREEGIM VKHPLSIYKP DKRGEGWLKI KPEYVSGLMD ELDVLIVGGY WGKGSRGGMM 490 500 510 520 530 540 SHFLCAVAET PPPGDRPSVF HTLCRVGSGY TMKELYDLGL KLAKYWKPFH KKSPPSSILC 550 560 570 580 590 600 GTEKPEVYIE PQNSVIVQIK AAEIVPSDMY KTGSTLRFPR IEKIRDDKEW HECMTLGDLE 610 620 630 640 650 660 QLRGKASGKL ATKHLHVGDD DEPREKRRKP ISKTKKAIRI IEHLKAPNLS NVNKVSNVFE 670 680 690 700 710 720 DVEFCVMSGL DGYPKADLEN RIAEFGGYIV QNPGPDTYCV IAGSENVRVK NIISSDKNDV 730 740 750 760 770 780 VKPEWLLECF KTKTCVPWQP RFMIHMCPST KQHFAREYDC YGDSYFVDTD LDQLKEVFLG 790 800 810 820 830 840 IKPSEQQTPE EMAPVIADLE CRYSWDHSPL SMFRHYTIYL DLYAVINDLS SRIEATRLGI 850 860 870 880 890 900 TALELRFHGA KVVSCLSEGV SHVIIGEDQR RVTDFKIFRR MLKKKFKILQ ESWVSDSVDK 910 GELQEENQYL L

References

[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]	"Lineage-specific biology revealed by a finished genome assembly of the mouse." Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X., Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y., Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S. , Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R., Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K., Eichler E.E., Ponting C.P. PLoS Biol. 7:E1000112-E1000112(2009) [PubMed] [Europe PMC] [Abstract] 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].
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	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.
IPI	IPI00225019.
RefSeq	NP_795927.2. NM_176953.3.
UniGene	Mm.80584.
3D structure databases
ProteinModelPortal	Q8BTF7.
SMR	Q8BTF7. Positions 8-607, 654-911.
ModBase	Search...
PTM databases
PhosphoSite	Q8BTF7.
Proteomic databases
PaxDb	Q8BTF7.
PRIDE	Q8BTF7.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
Ensembl	ENSMUST00000095476; ENSMUSP00000093130; ENSMUSG00000049717. ENSMUST00000170033; ENSMUSP00000130807; ENSMUSG00000049717.
GeneID	319583.
KEGG	mmu:319583.
UCSC	uc009kul.1. mouse.
Organism-specific databases
CTD	3981.
MGI	MGI:1335098. Lig4.
Phylogenomic databases
eggNOG	COG1793.
GeneTree	ENSGT00700000104500.
HOGENOM	HOG000007831.
HOVERGEN	HBG005516.
InParanoid	Q8BTF7.
KO	K10777.
OMA	HMCPSTK.
OrthoDB	EOG4Q58NP.
Gene expression databases
CleanEx	MM_LIG4.
Genevestigator	Q8BTF7.
GermOnline	ENSMUSG00000049717. Mus musculus.
Family and domain databases
Gene3D	1.10.3260.10. 1 hit. 2.40.50.140. 1 hit.
InterPro	IPR001357. 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. IPR012340. NA-bd_OB-fold. [Graphical view]
Pfam	PF00533. 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]
SMART	SM00292. BRCT. 2 hits. [Graphical view]
SUPFAM	SSF52113. BRCT. 2 hits. SSF50249. Nucleic_acid_OB. 1 hit. SSF117018. SSF117018. 1 hit.
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS50172. BRCT. 2 hits. PS00697. DNA_LIGASE_A1. 1 hit. PS00333. DNA_LIGASE_A2. 1 hit. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...
Other
NextBio	395028.
SOURCE	Search...

Entry information

Entry name

DNLI4_MOUSE

Accession

Primary (citable) accession number: Q8BTF7
Secondary accession number(s): G3UWC4, Q3UG76

Entry history

Integrated into UniProtKB/Swiss-Prot:	February 7, 2006
Last sequence update:	October 3, 2012
Last modified:	May 1, 2013
This is version 90 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program