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Protein

DNA ligase 4

Gene

lig4

Organism
Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Protein inferred from homologyi

Functioni

Involved in ds DNA break repair.3 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 sitei279 – 2791ATPBy similarity
Active sitei281 – 2811N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei286 – 2861ATPBy similarity
Binding sitei301 – 3011ATPBy similarity
Metal bindingi341 – 3411Magnesium 1Sequence analysis
Metal bindingi438 – 4381Magnesium 2Sequence analysis
Binding sitei443 – 4431ATPBy similarity
Binding sitei454 – 4541ATPBy similarity
Binding sitei460 – 4601ATPBy similarity

GO - Molecular functioni

GO - Biological processi

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

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
ORF Names:SPCC1183.05c
OrganismiSchizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast)
Taxonomic identifieri284812 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaTaphrinomycotinaSchizosaccharomycetesSchizosaccharomycetalesSchizosaccharomycetaceaeSchizosaccharomyces
Proteomesi
  • UP000002485 Componenti: Chromosome III

Organism-specific databases

EuPathDBiFungiDB:SPCC1183.05c.
PomBaseiSPCC1183.05c. lig4.

Subcellular locationi

GO - Cellular componenti

  • DNA ligase IV complex Source: PomBase
  • nuclear chromatin Source: PomBase
  • nucleolus Source: PomBase
  • nucleus Source: PomBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 913913DNA ligase 4PRO_0000059581Add
BLAST

Proteomic databases

PRIDEiO74833.

Interactioni

Protein-protein interaction databases

BioGridi275615. 6 interactions.

Structurei

3D structure databases

ProteinModelPortaliO74833.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini660 – 75394BRCT 1PROSITE-ProRule annotationAdd
BLAST
Domaini821 – 91393BRCT 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

InParanoidiO74833.
KOiK10777.
OMAiHPYEEAT.
OrthoDBiEOG7QC84G.

Family and domain databases

Gene3Di2.40.50.140. 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.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
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.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

O74833-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MDEAKETVFT KPQNHSSTLE FYDFVTTLLE PLSRIGKTRK SKTSNLDPYE
60 70 80 90 100
LKRKILLDYF NKWRQHVGPD LYPLLRLMLP DLDRERGSYG FKEFGLGKLF
110 120 130 140 150
IRAMHLSPTS EDAKSLKNWR GSESKHTGDF STMLQDILQR RAYRTFPGAF
160 170 180 190 200
TVGDVNALLD QLADASSEDT RVNILEQFYR SLSPLELRWL IPILLKVRKY
210 220 230 240 250
GTSEKFILSV FHPDAARLYR LCSSLKRICW ELYDPSRSLD ETETDVEVFS
260 270 280 290 300
CFQPQLANFK KKDLHQTLEA MGNKPFWIEE KLDGERIQLH MSSGKFQFYS
310 320 330 340 350
RNARSYTYAY GSSYFDEQSR LTQYIIGAFD KRISQIILDG EMVTWDPVLE
360 370 380 390 400
TVIPYGSLRS IFEDSSSHSS YSPYYVVFDI LYLNGKSLVK YSLESRRRIL
410 420 430 440 450
EKVIVRESHR MSILPYKVGS TIEDIEAELR NVIQEGSEGL VIKKPSGSYH
460 470 480 490 500
LGERMDDWIK VKPYYLQGFG EDLDCLILGG YFGRGKQSGK INSFLCGLRM
510 520 530 540 550
DYTPKDHSEK FQSFVRVGGG FTYFDRDIIR KETEGKWLPW SSDALEYMEL
560 570 580 590 600
AGTKQDFEKP DMWIHPKDSL VLQIKAAEVV VSNRFKTNYT LRFPRLEKVR
610 620 630 640 650
LDRSWKDALT INEFFTLKNA VEKQDNVSFH VNKKRKVSQK REKQKKFLYD
660 670 680 690 700
EPTFKKEASP HSDVLKNLHF VVLPPTELHE TKAGLQQIII ENGGLIHQGV
710 720 730 740 750
GNFGKERLFL VADRVSTRVS IERSKNMCTI IRSQWVMDSV NNQRLMPQWS
760 770 780 790 800
YLLFSKDEKY SWKTALESLS AKSLSNLLVE LKQLDLSKEY SKISDDTSIL
810 820 830 840 850
NLTISKEEAS FVGAFPFLKF TVFLDLKGIE NSELYDVRMG QYRLTKCILL
860 870 880 890 900
WNGATIEKDI SSKKLTHVVM FVEDSTRLEQ LTKACELYQI EPKFVNFEWV
910
VNEWKKASTN ILG
Length:913
Mass (Da):106,025
Last modified:July 11, 2012 - v3
Checksum:i18891DCE634EB752
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329672 Genomic DNA. Translation: CAA21085.3.
PIRiT40845.
RefSeqiNP_587888.2. NM_001022880.2.

Genome annotation databases

EnsemblFungiiSPCC1183.05c.1; SPCC1183.05c.1:pep; SPCC1183.05c.
GeneIDi2539042.
KEGGispo:SPCC1183.05c.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CU329672 Genomic DNA. Translation: CAA21085.3.
PIRiT40845.
RefSeqiNP_587888.2. NM_001022880.2.

3D structure databases

ProteinModelPortaliO74833.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi275615. 6 interactions.

Proteomic databases

PRIDEiO74833.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiSPCC1183.05c.1; SPCC1183.05c.1:pep; SPCC1183.05c.
GeneIDi2539042.
KEGGispo:SPCC1183.05c.

Organism-specific databases

EuPathDBiFungiDB:SPCC1183.05c.
PomBaseiSPCC1183.05c. lig4.

Phylogenomic databases

InParanoidiO74833.
KOiK10777.
OMAiHPYEEAT.
OrthoDBiEOG7QC84G.

Miscellaneous databases

NextBioi20800216.
PROiO74833.

Family and domain databases

Gene3Di2.40.50.140. 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.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
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.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The genome sequence of Schizosaccharomyces pombe."
    Wood V., Gwilliam R., Rajandream M.A., Lyne M.H., Lyne R., Stewart A., Sgouros J.G., Peat N., Hayles J., Baker S.G., Basham D., Bowman S., Brooks K., Brown D., Brown S., Chillingworth T., Churcher C.M., Collins M.
    , Connor R., Cronin A., Davis P., Feltwell T., Fraser A., Gentles S., Goble A., Hamlin N., Harris D.E., Hidalgo J., Hodgson G., Holroyd S., Hornsby T., Howarth S., Huckle E.J., Hunt S., Jagels K., James K.D., Jones L., Jones M., Leather S., McDonald S., McLean J., Mooney P., Moule S., Mungall K.L., Murphy L.D., Niblett D., Odell C., Oliver K., O'Neil S., Pearson D., Quail M.A., Rabbinowitsch E., Rutherford K.M., Rutter S., Saunders D., Seeger K., Sharp S., Skelton J., Simmonds M.N., Squares R., Squares S., Stevens K., Taylor K., Taylor R.G., Tivey A., Walsh S.V., Warren T., Whitehead S., Woodward J.R., Volckaert G., Aert R., Robben J., Grymonprez B., Weltjens I., Vanstreels E., Rieger M., Schaefer M., Mueller-Auer S., Gabel C., Fuchs M., Duesterhoeft A., Fritzc C., Holzer E., Moestl D., Hilbert H., Borzym K., Langer I., Beck A., Lehrach H., Reinhardt R., Pohl T.M., Eger P., Zimmermann W., Wedler H., Wambutt R., Purnelle B., Goffeau A., Cadieu E., Dreano S., Gloux S., Lelaure V., Mottier S., Galibert F., Aves S.J., Xiang Z., Hunt C., Moore K., Hurst S.M., Lucas M., Rochet M., Gaillardin C., Tallada V.A., Garzon A., Thode G., Daga R.R., Cruzado L., Jimenez J., Sanchez M., del Rey F., Benito J., Dominguez A., Revuelta J.L., Moreno S., Armstrong J., Forsburg S.L., Cerutti L., Lowe T., McCombie W.R., Paulsen I., Potashkin J., Shpakovski G.V., Ussery D., Barrell B.G., Nurse P.
    Nature 415:871-880(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 972 / ATCC 24843.
  2. "Comparative functional genomics of the fission yeasts."
    Rhind N., Chen Z., Yassour M., Thompson D.A., Haas B.J., Habib N., Wapinski I., Roy S., Lin M.F., Heiman D.I., Young S.K., Furuya K., Guo Y., Pidoux A., Chen H.M., Robbertse B., Goldberg J.M., Aoki K.
    , Bayne E.H., Berlin A.M., Desjardins C.A., Dobbs E., Dukaj L., Fan L., FitzGerald M.G., French C., Gujja S., Hansen K., Keifenheim D., Levin J.Z., Mosher R.A., Mueller C.A., Pfiffner J., Priest M., Russ C., Smialowska A., Swoboda P., Sykes S.M., Vaughn M., Vengrova S., Yoder R., Zeng Q., Allshire R., Baulcombe D., Birren B.W., Brown W., Ekwall K., Kellis M., Leatherwood J., Levin H., Margalit H., Martienssen R., Nieduszynski C.A., Spatafora J.W., Friedman N., Dalgaard J.Z., Baumann P., Niki H., Regev A., Nusbaum C.
    Science 332:930-936(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVISION OF GENE MODEL.
  3. "Protection of telomeres by the Ku protein in fission yeast."
    Baumann P., Cech T.R.
    Mol. Biol. Cell 11:3265-3275(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  4. "The fission yeast Taz1 protein protects chromosomes from Ku-dependent end-to-end fusions."
    Ferreira M.G., Cooper J.P.
    Mol. Cell 7:55-63(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.
  5. "Histone H2A phosphorylation controls Crb2 recruitment at DNA breaks, maintains checkpoint arrest, and influences DNA repair in fission yeast."
    Nakamura T.M., Du L.-L., Redon C., Russell P.
    Mol. Cell. Biol. 24:6215-6230(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiDNLI4_SCHPO
AccessioniPrimary (citable) accession number: O74833
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 7, 2006
Last sequence update: July 11, 2012
Last modified: May 11, 2016
This is version 109 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Schizosaccharomyces pombe
    Schizosaccharomyces pombe: 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.