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Q08387 (DNLI4_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 124. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (4) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA ligase 4

EC=6.5.1.1
Alternative name(s):
DNA ligase II
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4
Gene names
Name:DNL4
Synonyms:LIG4
Ordered Locus Names:YOR005C
ORF Names:UND407, UNE452
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length944 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Has minor DNA joining activity. Can act on oligo(PDT)/poly(rA) substrate.

Catalytic activity

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).

Cofactor

Magnesium By similarity.

Subunit structure

Interacts with LIF1 via its BRCT domain. Interacts with POL4 in the DNL4-LIF1 complex. Ref.5 Ref.6

Subcellular location

Nucleus Potential.

Sequence similarities

Belongs to the ATP-dependent DNA ligase family.

Contains 2 BRCT domains.

Sequence caution

The sequence AAC49484.1 differs from that shown. Reason: Frameshift at positions 408 and 413. Produces 2 separate ORFs.

The sequence AAC49485.1 differs from that shown. Reason: Frameshift at positions 408 and 413. Produces 2 separate ORFs.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 944944DNA ligase 4
PRO_0000059582

Regions

Domain681 – 780100BRCT 1
Domain836 – 941106BRCT 2

Sites

Active site2821N6-AMP-lysine intermediate By similarity
Metal binding3401Magnesium 1 Potential
Metal binding4421Magnesium 2 Potential
Binding site2801ATP By similarity
Binding site2871ATP By similarity
Binding site3041ATP By similarity
Binding site4471ATP By similarity
Binding site4581ATP By similarity
Binding site4641ATP By similarity

Secondary structure

......................................... 944
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
Q08387 [UniParc].

Last modified November 1, 1996. Version 1.
Checksum: 7FB6D7927E1719B5

FASTA944108,515
        10         20         30         40         50         60 
MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY YEIISNFVEM 

        70         80         90        100        110        120 
WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL KLPKNSATEQ RLKDWKQRVG 

       130        140        150        160        170        180 
KGGNLSSLLV EEIAKRRAEP SSKAITIDNV NHYLDSLSGD RFASGRGFKS LVKSKPFLHC 

       190        200        210        220        230        240 
VENMSFVELK YFFDIVLKNR VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR 

       250        260        270        280        290        300 
LKDDDLSIKV GFAFAPQLAK KVNLSYEKIC RTLHDDFLVE EKMDGERIQV HYMNYGESIK 

       310        320        330        340        350        360 
FFSRRGIDYT YLYGASLSSG TISQHLRFTD SVKECVLDGE MVTFDAKRRV ILPFGLVKGS 

       370        380        390        400        410        420 
AKEALSFNSI NNVDFHPLYM VFDLLYLNGT SLTPLPLHQR KQYLNSILSP LKNIVEIVRS 

       430        440        450        460        470        480 
SRCYGVESIK KSLEVAISLG SEGVVLKYYN SSYNVASRNN NWIKVKPEYL EEFGENLDLI 

       490        500        510        520        530        540 
VIGRDSGKKD SFMLGLLVLD EEEYKKHQGD SSEIVDHSSQ EKHIQNSRRR VKKILSFCSI 

       550        560        570        580        590        600 
ANGISQEEFK EIDRKTRGHW KRTSEVAPPA SILEFGSKIP AEWIDPSESI VLEIKSRSLD 

       610        620        630        640        650        660 
NTETNMQKYA TNCTLYGGYC KRIRYDKEWT DCYTLNDLYE SRTVKSNPSY QAERSQLGLI 

       670        680        690        700        710        720 
RKKRKRVLIS DSFHQNRKQL PISNIFAGLL FYVLSDYVTE DTGIRITRAE LEKTIVEHGG 

       730        740        750        760        770        780 
KLIYNVILKR HSIGDVRLIS CKTTTECKAL IDRGYDILHP NWVLDCIAYK RLILIEPNYC 

       790        800        810        820        830        840 
FNVSQKMRAV AEKRVDCLGD SFENDISETK LSSLYKSQLS LPPMGELEID SEVRRFPLFL 

       850        860        870        880        890        900 
FSNRIAYVPR RKISTEDDII EMKIKLFGGK ITDQQSLCNL IIIPYTDPIL RKDCMNEVHE 

       910        920        930        940 
KIKEQIKASD TIPKIARVVA PEWVDHSINE NCQVPEEDFP VVNY 

« Hide

References

« Hide 'large scale' references
[1]"The sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes."
Sterky F., Holmberg A., Pettersson B., Uhlen M.
Yeast 12:1091-1095(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D. expand/collapse author list , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Two distinct DNA ligase activities in mitotic extracts of the yeast Saccharomyces cerevisiae."
Ramos W., Tappe N., Talamantez J., Friedberg E.C., Tomkinson A.E.
Nucleic Acids Res. 25:1485-1492(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[5]"Saccharomyces cerevisiae LIF1: a function involved in DNA double-strand break repair related to mammalian XRCC4."
Herrmann G., Lindahl T., Schar P.
EMBO J. 17:4188-4198(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH LIF1.
[6]"A physical and functional interaction between yeast Pol4 and Dnl4-Lif1 links DNA synthesis and ligation in nonhomologous end joining."
Tseng H.-M., Tomkinson A.E.
J. Biol. Chem. 277:45630-45637(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH POL4.
[7]"Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode."
Dore A.S., Furnham N., Davies O.R., Sibanda B.L., Chirgadze D.Y., Jackson S.P., Pellegrini L., Blundell T.L.
DNA Repair 5:362-368(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (3.92 ANGSTROMS) OF 681-944 IN COMPLEX WITH LIF1.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
U43491 Genomic DNA. Translation: AAC49485.1. Frameshift.
U43491 Genomic DNA. Translation: AAC49484.1. Frameshift.
Z74913 Genomic DNA. Translation: CAA99193.1.
BK006948 Genomic DNA. Translation: DAA10787.1.
PIRS66870.
RefSeqNP_014647.1. NM_001183424.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1Z56X-ray3.92C681-944[»]
ProteinModelPortalQ08387.
SMRQ08387. Positions 13-642, 683-939.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid34408. 47 interactions.
DIPDIP-5801N.
IntActQ08387. 1 interaction.
MINTMINT-672762.
STRING4932.YOR005C.

Proteomic databases

PaxDbQ08387.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYOR005C; YOR005C; YOR005C.
GeneID854166.
KEGGsce:YOR005C.

Organism-specific databases

CYGDYOR005c.
SGDS000005531. DNL4.

Phylogenomic databases

eggNOGCOG1793.
GeneTreeENSGT00750000117695.
HOGENOMHOG000093622.
KOK10777.
OMAHSINENC.
OrthoDBEOG7QC84G.

Enzyme and pathway databases

BioCycYEAST:G3O-33555-MONOMER.
BRENDA6.5.1.1. 984.

Gene expression databases

GenevestigatorQ08387.

Family and domain databases

Gene3D2.40.50.140. 1 hit.
InterProIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
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]
PfamPF00533. BRCT. 2 hits.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SMARTSM00292. BRCT. 1 hit.
[Graphical view]
SUPFAMSSF50249. SSF50249. 2 hits.
SSF52113. SSF52113. 3 hits.
TIGRFAMsTIGR00574. dnl1. 1 hit.
PROSITEPS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceQ08387.
NextBio975950.
PROQ08387.

Entry information

Entry nameDNLI4_YEAST
AccessionPrimary (citable) accession number: Q08387
Secondary accession number(s): D6W271, Q02913, Q02914
Entry history
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: April 16, 2014
This is version 124 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XV

Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Yeast

Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references