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P35732 (DEF1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified May 29, 2013. Version 100. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order
to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
RNA polymerase II degradation factor 1
Alternative name(s):
RRM3-interacting protein 1
Gene names
Name:DEF1
Synonyms:RIP1, VID31
Ordered Locus Names:YKL054C
ORF Names:YKL308
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces ›

Protein attributes

Sequence length738 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

RNA polymerase II degradation factor recruits the ubiquitination machinery to the RNA polymerase II for polyubiquitination, removal and degradation, when RAD26 fails to efficiently displace stalled RNA polymerase II. Also involved in telomere length regulation. Ref.4 Ref.6 Ref.7 Ref.8

Subunit structure

Interacts with the RNA polymerase II in a DNA-damaged dependent manner. Interacts with RAD26. Binds DNA. Ref.4 Ref.6 Ref.8

Subcellular location

Nucleus. Chromosome › telomere Ref.8.

Miscellaneous

Present with 3380 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the DEF1 family.

Contains 1 CUE domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 738738RNA polymerase II degradation factor 1
PRO_0000203177

Regions

Domain21 – 6343CUE
Compositional bias382 – 718337Gln-rich
Compositional bias574 – 5807Poly-Ala
Compositional bias708 – 7169Poly-Ala

Amino acid modifications

Modified residue1081Phosphoserine Ref.12
Modified residue1101Phosphoserine Ref.12
Modified residue1181Phosphoserine Ref.12
Modified residue2601Phosphoserine Ref.9 Ref.10 Ref.11 Ref.12
Modified residue2731Phosphoserine Ref.10 Ref.11
Modified residue3381Phosphothreonine Ref.12
Modified residue4941Phosphoserine Ref.12
Modified residue4971Phosphoserine Ref.12
Modified residue6461Phosphoserine Ref.9 Ref.11 Ref.12

Sequences

Sequence LengthMass (Da)Tools
P35732 [UniParc].

Last modified June 1, 1994. Version 1.
Checksum: 05734E2D0B7389AC

FASTA73883,973
        10         20         30         40         50         60 
MSTQFRKSNH NSHSSKKLNP ALKSKIDTLT ELFPDWTSDD LIDIVQEYDD LETIIDKITS 

        70         80         90        100        110        120 
GAVTRWDEVK KPAKKEKYEK KEQQHSYVPQ QHLPNPEDDI TYKSSNNSNS FTSTKHNSSN 

       130        140        150        160        170        180 
NYTQARNKKK VQTPRAHTTG KHVNLDKGKH VPSKPVSNTT SWAAAVSVDT KHDVPQDSND 

       190        200        210        220        230        240 
NNNEELEAQG QQAQEKNQEK EQEEQQQQEG HNNKEEHKQI EQPSLSSKKT TSRTSASQPK 

       250        260        270        280        290        300 
KMSWAAIATP KPKAVKKTES PLENVAELKK EISDIKKDDQ KSEASEEKVN EQETSAQEQE 

       310        320        330        340        350        360 
EETAEPSEEN EDRVPEVDGE EVQEEAEKKE QVKEEEQTAE ELEQEQDNVA APEEEVTVVE 

       370        380        390        400        410        420 
EKVEISAVIS EPPEDQANTV PQPQQQSQQP QQPQQPQQPQ QPQQPQQQQQ PQQPQQPQQQ 

       430        440        450        460        470        480 
LQQQQQQQQQ PVQAQAQAQE EQLSQNYYTQ QQQQQYAQQQ HQLQQQYLSQ QQQYAQQQQQ 

       490        500        510        520        530        540 
HPQPQSQQPQ SQQSPQSQKQ GNNVAAQQYY MYQNQFPGYS YPGMFDSQGY AYGQQYQQLA 

       550        560        570        580        590        600 
QNNAQTSGNA NQYNFQQGYG QAGANTAAAN LTSAAAAAAA SPATAHAQPQ QQQPYGGSFM 

       610        620        630        640        650        660 
PYYAHFYQQS FPYGQPQYGV AGQYPYQLPK NNYNYYQTQN GQEQQSPNQG VAQHSEDSQQ 

       670        680        690        700        710        720 
KQSQQQQQQQ PQGQPQPEVQ MQNGQPVNPQ QQMQFQQYYQ FQQQQQQAAA AAAAAAQQGV 

       730 
PYGYNGYDYN SKNSRGFY

« Hide

References

« Hide 'large scale' references
[1]"Sequence of a 28.6 kb region of yeast chromosome XI includes the FBA1 and TOA2 genes, an open reading frame (ORF) similar to a translationally controlled tumour protein, one ORF containing motifs also found in plant storage proteins and 13 ORFs with weak or no homology to known proteins."
Rasmussen S.W.
Yeast 10:S63-S68(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[2]"Complete DNA sequence of yeast chromosome XI."
Dujon B., Alexandraki D., Andre B., Ansorge W., Baladron V., Ballesta J.P.G., Banrevi A., Bolle P.-A., Bolotin-Fukuhara M., Bossier P., Bou G., Boyer J., Buitrago M.J., Cheret G., Colleaux L., Daignan-Fornier B., del Rey F., Dion C. expand/collapse author list , Domdey H., Duesterhoeft A., Duesterhus S., Entian K.-D., Erfle H., Esteban P.F., Feldmann H., Fernandes L., Fobo G.M., Fritz C., Fukuhara H., Gabel C., Gaillon L., Garcia-Cantalejo J.M., Garcia-Ramirez J.J., Gent M.E., Ghazvini M., Goffeau A., Gonzalez A., Grothues D., Guerreiro P., Hegemann J.H., Hewitt N., Hilger F., Hollenberg C.P., Horaitis O., Indge K.J., Jacquier A., James C.M., Jauniaux J.-C., Jimenez A., Keuchel H., Kirchrath L., Kleine K., Koetter P., Legrain P., Liebl S., Louis E.J., Maia e Silva A., Marck C., Monnier A.-L., Moestl D., Mueller S., Obermaier B., Oliver S.G., Pallier C., Pascolo S., Pfeiffer F., Philippsen P., Planta R.J., Pohl F.M., Pohl T.M., Poehlmann R., Portetelle D., Purnelle B., Puzos V., Ramezani Rad M., Rasmussen S.W., Remacha M.A., Revuelta J.L., Richard G.-F., Rieger M., Rodrigues-Pousada C., Rose M., Rupp T., Santos M.A., Schwager C., Sensen C., Skala J., Soares H., Sor F., Stegemann J., Tettelin H., Thierry A., Tzermia M., Urrestarazu L.A., van Dyck L., van Vliet-Reedijk J.C., Valens M., Vandenbol M., Vilela C., Vissers S., von Wettstein D., Voss H., Wiemann S., Xu G., Zimmermann J., Haasemann M., Becker I., Mewes H.-W.
Nature 369:371-378(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 96604 / S288c / FY1679.
[3]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"A Rad26-Def1 complex coordinates repair and RNA pol II proteolysis in response to DNA damage."
Woudstra E.C., Gilbert C., Fellows J., Jansen L., Brouwer J., Erdjument-Bromage H., Tempst P., Svejstrup J.Q.
Nature 415:929-933(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RAD26, FUNCTION.
[5]"Global analysis of protein expression in yeast."
Ghaemmaghami S., Huh W.-K., Bower K., Howson R.W., Belle A., Dephoure N., O'Shea E.K., Weissman J.S.
Nature 425:737-741(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: LEVEL OF PROTEIN EXPRESSION [LARGE SCALE ANALYSIS].
[6]"DNA damage-induced Def1-RNA polymerase II interaction and Def1 requirement for polymerase ubiquitylation in vitro."
Reid J., Svejstrup J.Q.
J. Biol. Chem. 279:29875-29878(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH RNA POLYMERASE II, FUNCTION.
[7]"Multiple mechanisms confining RNA polymerase II ubiquitylation to polymerases undergoing transcriptional arrest."
Somesh B.P., Reid J., Liu W.F., Sogaard T.M., Erdjument-Bromage H., Tempst P., Svejstrup J.Q.
Cell 121:913-923(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[8]"Def1p is involved in telomere maintenance in budding yeast."
Chen Y.B., Yang C.P., Li R.X., Zeng R., Zhou J.Q.
J. Biol. Chem. 280:24784-24791(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: MASS SPECTROMETRY, INTERACTION WITH RRM3, SUBCELLULAR LOCATION, DNA-BINDING, FUNCTION.
[9]"Large-scale phosphorylation analysis of alpha-factor-arrested Saccharomyces cerevisiae."
Li X., Gerber S.A., Rudner A.D., Beausoleil S.A., Haas W., Villen J., Elias J.E., Gygi S.P.
J. Proteome Res. 6:1190-1197(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260 AND SER-646, MASS SPECTROMETRY.
Strain: ADR376.
[10]"Analysis of phosphorylation sites on proteins from Saccharomyces cerevisiae by electron transfer dissociation (ETD) mass spectrometry."
Chi A., Huttenhower C., Geer L.Y., Coon J.J., Syka J.E.P., Bai D.L., Shabanowitz J., Burke D.J., Troyanskaya O.G., Hunt D.F.
Proc. Natl. Acad. Sci. U.S.A. 104:2193-2198(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260 AND SER-273, MASS SPECTROMETRY.
[11]"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases."
Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H.
Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-260; SER-273 AND SER-646, MASS SPECTROMETRY.
[12]"A multidimensional chromatography technology for in-depth phosphoproteome analysis."
Albuquerque C.P., Smolka M.B., Payne S.H., Bafna V., Eng J., Zhou H.
Mol. Cell. Proteomics 7:1389-1396(2008) [PubMed] [Europe PMC] [Abstract]
Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-108; SER-110; SER-118; SER-260; THR-338; SER-494; SER-497 AND SER-646, MASS SPECTROMETRY.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		X75781 Genomic DNA. Translation: CAA53418.1.
Z28054 Genomic DNA. Translation: CAA81890.1.
BK006944 Genomic DNA. Translation: DAA09103.1.
PIRS37876.
RefSeqNP_012869.1. NM_001179620.1.

3D structure databases

ProteinModelPortalP35732.
ModBaseSearch...

Protein-protein interaction databases

DIPDIP-6354N.
IntActP35732. 40 interactions.
MINTMINT-693440.
STRING4932.YKL054C.

Proteomic databases

PaxDbP35732.
PeptideAtlasP35732.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYKL054C; YKL054C; YKL054C.
GeneID853811.
KEGGsce:YKL054C.

Organism-specific databases

CYGDYKL054c.
SGDS000001537. DEF1.

Phylogenomic databases

eggNOGNOG16498.
GeneTreeENSGT00670000098037.
OMADREEPET.
OrthoDBEOG44QX9T.

Enzyme and pathway databases

BioCycYEAST:G3O-31854-MONOMER.

Gene expression databases

GenevestigatorP35732.
GermOnlineYKL054C. Saccharomyces cerevisiae.

Family and domain databases

InterProIPR003892. CUE.
[Graphical view]
PfamPF02845. CUE. 1 hit.
[Graphical view]
PROSITEPS51140. CUE. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

NextBio974978.

Entry information

Entry nameDEF1_YEAST
AccessionPrimary (citable) accession number: P35732
Secondary accession number(s): D6VXN3
Entry history
Integrated into UniProtKB/Swiss-Prot: June 1, 1994
Last sequence update: June 1, 1994
Last modified: May 29, 2013
This is version 100 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast

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

Yeast chromosome XI

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

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents