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P11938 (RAP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 152. 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·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
DNA-binding protein RAP1
Alternative name(s):
Repressor/activator site-binding protein
SBF-E
TUF
Gene names
Name:RAP1
Synonyms:GRF1, TUF1
Ordered Locus Names:YNL216W
ORF Names:N1310
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length827 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Essential regulatory protein in yeast whose DNA-binding sites are found at three types of chromosomal elements: promoters, silencers, and telomeres. RAP1 is also involved in the regulation of telomere structure, where its binding sites are found within the terminal poly[C1-3A] sequences. The opposite regulatory functions of RAP1 are not intrinsic to its binding sites but, instead, result from interactions with different factors at promoters and silencers. RAP1 associates with SIR3 and SIR4 proteins to form a DNA-binding complex that initiates the repression at the HM loci and telomeres. May also target the binding of RIF1 and RIF2 to silencers and telomeres. Forms with GCR1 a transcriptional activation complex that is required for expression of glycolytic and ribosomal gene.

Subunit structure

RIF1, SIR3 and SIR4 associate with RAP1 C-terminus in vivo. Interacts with a GCR1 homodimer. Ref.5

Subcellular location

Nucleus. Chromosometelomere.

Miscellaneous

Present with 4390 molecules/cell in log phase SD medium.

Sequence similarities

Belongs to the RAP1 family.

Contains 1 BRCT domain.

Contains 1 HTH myb-type DNA-binding domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentChromosome
Nucleus
Telomere
   LigandDNA-binding
   Molecular functionActivator
Repressor
   PTMPhosphoprotein
   Technical term3D-structure
Complete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processchromatin silencing at silent mating-type cassette

Inferred from genetic interaction PubMed 7958893. Source: SGD

chromatin silencing at telomere

Inferred from genetic interaction PubMed 7958893. Source: SGD

establishment of chromatin silencing at telomere

Inferred from physical interaction PubMed 12080091. Source: SGD

establishment of protein localization to chromatin

Inferred from physical interaction PubMed 11689698. Source: SGD

establishment of protein localization to telomere

Inferred from physical interaction PubMed 11689698. Source: SGD

negative regulation of chromatin silencing

Inferred from direct assay PubMed 12582242. Source: SGD

negative regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 2010087. Source: SGD

positive regulation of transcription from RNA polymerase II promoter

Inferred from mutant phenotype PubMed 2010087. Source: SGD

protection from non-homologous end joining at telomere

Inferred from mutant phenotype PubMed 16096640. Source: SGD

regulation of glycolysis by positive regulation of transcription from RNA polymerase II promoter

Inferred from genetic interaction PubMed 15300680. Source: SGD

regulation of transcription by chromatin organization

Inferred from direct assay PubMed 10409719. Source: SGD

telomere maintenance

Inferred from mutant phenotype PubMed 2237406. Source: SGD

telomere maintenance via telomere lengthening

Inferred from direct assay PubMed 9020083. Source: SGD

transcription from RNA polymerase II promoter

Inferred from direct assay PubMed 18195009PubMed 1904543PubMed 20559389. Source: GOC

   Cellular_componentcytosol

Inferred from direct assay PubMed 22932476. Source: SGD

nuclear chromosome

Inferred from direct assay PubMed 11455386. Source: SGD

nuclear chromosome, telomeric region

Inferred from direct assay PubMed 16956377PubMed 9710643. Source: SGD

nuclear nucleosome

Inferred from direct assay. Source: SGD

nuclear telomere cap complex

Inferred from direct assay. Source: SGD

nucleus

Inferred from direct assay PubMed 22932476. Source: SGD

   Molecular_functionDNA binding, bending

Inferred from direct assay PubMed 2656680. Source: SGD

G-quadruplex DNA binding

Inferred from direct assay Ref.6. Source: SGD

RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity

Inferred from direct assay PubMed 1904543. Source: SGD

RNA polymerase II transcription factor binding transcription factor activity

Inferred from direct assay PubMed 20559389. Source: SGD

TBP-class protein binding RNA polymerase II transcription factor activity

Inferred from direct assay PubMed 18195009. Source: SGD

TFIID-class transcription factor binding

Inferred from direct assay PubMed 17074814. Source: SGD

core promoter proximal region sequence-specific DNA binding

Inferred from direct assay PubMed 12051841. Source: SGD

nucleosomal DNA binding

Inferred from direct assay PubMed 19782036. Source: SGD

telomeric DNA binding

Inferred from direct assay PubMed 17656141PubMed 8510148. Source: SGD

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 827827DNA-binding protein RAP1
PRO_0000197112

Regions

Domain121 – 20888BRCT
Domain355 – 41561HTH myb-type
DNA binding388 – 41124H-T-H motif
Region630 – 69566Activation domain
Compositional bias71 – 744Poly-Asp
Compositional bias81 – 844Poly-Thr
Compositional bias313 – 3208Poly-Asn
Compositional bias614 – 62714Poly-Ala

Amino acid modifications

Modified residue4861Phosphothreonine Ref.8
Modified residue7311Phosphoserine Ref.9

Experimental info

Sequence conflict6721A → R in AAA18404. Ref.1

Secondary structure

.......................................................... 827
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P11938 [UniParc].

Last modified February 1, 1995. Version 2.
Checksum: 67C4AFB03B3C0713

FASTA82792,413
        10         20         30         40         50         60 
MSSPDDFETA PAEYVDALDP SMVVVDSGSA AVTAPSDSAA EVKANQNEEN TGATAAETSE 

        70         80         90        100        110        120 
KVDQTEVEKK DDDDTTEVGV TTTTPSIADT AATANIASTS GASVTEPTTD DTAADEKKEQ 

       130        140        150        160        170        180 
VSGPPLSNMK FYLNRDADAH DSLNDIDQLA RLIRANGGEV LDSKPRESKE NVFIVSPYNH 

       190        200        210        220        230        240 
TNLPTVTPTY IKACCQSNSL LNMENYLVPY DNFREVVDSR LQEESHSNGV DNSNSNSDNK 

       250        260        270        280        290        300 
DSIRPKTEII STNTNGATED STSEKVMVDA EQQARLQEQA QLLRQHVSST ASITSGGHND 

       310        320        330        340        350        360 
LVQIEQPQKD TSNNNNSNVN DEDNDLLTQD NNPQTADEGN ASFQAQRSMI SRGALPSHNK 

       370        380        390        400        410        420 
ASFTDEEDEF ILDVVRKNPT RRTTHTLYDE ISHYVPNHTG NSIRHRFRVY LSKRLEYVYE 

       430        440        450        460        470        480 
VDKFGKLVRD DDGNLIKTKV LPPSIKRKFS ADEDYTLAIA VKKQFYRDLF QIDPDTGRSL 

       490        500        510        520        530        540 
ITDEDTPTAI ARRNMTMDPN HVPGSEPNFA AYRTQSRRGP IAREFFKHFA EEHAAHTENA 

       550        560        570        580        590        600 
WRDRFRKFLL AYGIDDYISY YEAEKAQNRE PEPMKNLTNR PKRPGVPTPG NYNSAAKRAR 

       610        620        630        640        650        660 
NYSSQRNVQP TANAASANAA AAAAAAASNS YAIPENELLD EDTMNFISSL KNDLSNISNS 

       670        680        690        700        710        720 
LPFEYPHEIA EAIRSDFSNE DIYDNIDPDT ISFPPKIATT DLFLPLFFHF GSTRQFMDKL 

       730        740        750        760        770        780 
HEVISGDYEP SQAEKLVQDL CDETGIRKNF STSILTCLSG DLMVFPRYFL NMFKDNVNPP 

       790        800        810        820 
PNVPGIWTHD DDESLKSNDQ EQIRKLVKKH GTGRMEMRKR FFEKDLL 

« Hide

References

« Hide 'large scale' references
[1]"Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements."
Shore D., Nasmyth K.
Cell 51:721-732(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: BJ2168.
[2]"The sequence of a 13.5 kb DNA segment from the left arm of yeast chromosome XIV reveals MER1; RAP1; a new putative member of the DNA replication complex and a new putative serine/threonine phosphatase gene."
Coster F., van Dyck L., Jonniaux J.-L., Purnelle B., Goffeau A.
Yeast 11:85-91(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 96604 / S288c / FY1679.
[3]"The nucleotide sequence of Saccharomyces cerevisiae chromosome XIV and its evolutionary implications."
Philippsen P., Kleine K., Poehlmann R., Duesterhoeft A., Hamberg K., Hegemann J.H., Obermaier B., Urrestarazu L.A., Aert R., Albermann K., Altmann R., Andre B., Baladron V., Ballesta J.P.G., Becam A.-M., Beinhauer J.D., Boskovic J., Buitrago M.J. expand/collapse author list , Bussereau F., Coster F., Crouzet M., D'Angelo M., Dal Pero F., De Antoni A., del Rey F., Doignon F., Domdey H., Dubois E., Fiedler T.A., Fleig U., Floeth M., Fritz C., Gaillardin C., Garcia-Cantalejo J.M., Glansdorff N., Goffeau A., Gueldener U., Herbert C.J., Heumann K., Heuss-Neitzel D., Hilbert H., Hinni K., Iraqui Houssaini I., Jacquet M., Jimenez A., Jonniaux J.-L., Karpfinger-Hartl L., Lanfranchi G., Lepingle A., Levesque H., Lyck R., Maftahi M., Mallet L., Maurer C.T.C., Messenguy F., Mewes H.-W., Moestl D., Nasr F., Nicaud J.-M., Niedenthal R.K., Pandolfo D., Pierard A., Piravandi E., Planta R.J., Pohl T.M., Purnelle B., Rebischung C., Remacha M.A., Revuelta J.L., Rinke M., Saiz J.E., Sartorello F., Scherens B., Sen-Gupta M., Soler-Mira A., Urbanus J.H.M., Valle G., Van Dyck L., Verhasselt P., Vierendeels F., Vissers S., Voet M., Volckaert G., Wach A., Wambutt R., Wedler H., Zollner A., Hani J.
Nature 387:93-98(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[4]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[5]"GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain."
Tornow J., Zeng X., Gao W., Santangelo G.M.
EMBO J. 12:2431-2437(1993) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH GCR1.
[6]"The yeast telomere-binding protein RAP1 binds to and promotes the formation of DNA quadruplexes in telomeric DNA."
Giraldo R., Rhodes D.
EMBO J. 13:2411-2420(1994) [PubMed] [Europe PMC] [Abstract]
Cited for: CHARACTERIZATION.
[7]"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].
[8]"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 THR-486, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
Strain: ADR376.
[9]"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-731, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[10]"Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution."
Holt L.J., Tuch B.B., Villen J., Johnson A.D., Gygi S.P., Morgan D.O.
Science 325:1682-1686(2009) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[11]"The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA."
Koenig P., Giraldo R., Chapman L., Rhodes D.
Cell 85:125-136(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.25 ANGSTROMS) OF 360-600.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
M18068 Unassigned DNA. Translation: AAA18404.1.
X78898 Genomic DNA. Translation: CAA55491.1.
Z71492 Genomic DNA. Translation: CAA96118.1.
BK006947 Genomic DNA. Translation: DAA10340.1.
PIRS50714.
RefSeqNP_014183.1. NM_001183054.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1IGNX-ray2.25A/B353-598[»]
2L42NMR-A116-212[»]
3CZ6X-ray1.85A/B672-827[»]
3OWTX-ray2.00A/B672-827[»]
3UKGX-ray2.95A360-601[»]
4BJ5X-ray3.29C/E627-827[»]
4BJ6X-ray3.26C/E627-827[»]
4BJTX-ray1.61A/B/C627-827[»]
4GFBX-ray2.99A358-602[»]
DisProtDP00020.
ProteinModelPortalP11938.
SMRP11938. Positions 116-212, 360-601, 676-827.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid35620. 277 interactions.
DIPDIP-851N.
IntActP11938. 46 interactions.
MINTMINT-551528.
STRING4932.YNL216W.

Proteomic databases

PaxDbP11938.
PeptideAtlasP11938.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYNL216W; YNL216W; YNL216W.
GeneID855505.
KEGGsce:YNL216W.

Organism-specific databases

CYGDYNL216w.
SGDS000005160. RAP1.

Phylogenomic databases

eggNOGNOG46211.
HOGENOMHOG000115833.
KOK09426.
OMAIAREFFK.
OrthoDBEOG74J9HM.

Enzyme and pathway databases

BioCycYEAST:G3O-33222-MONOMER.

Gene expression databases

GenevestigatorP11938.

Family and domain databases

Gene3D1.10.10.60. 3 hits.
3.40.50.10190. 1 hit.
InterProIPR001357. BRCT_dom.
IPR009057. Homeodomain-like.
IPR017930. Myb_dom.
IPR021661. Rap1_C.
IPR015280. Rap1_DNA-bd.
IPR001005. SANT/Myb.
[Graphical view]
PfamPF00249. Myb_DNA-binding. 1 hit.
PF09197. Rap1-DNA-bind. 1 hit.
PF11626. Rap1_C. 1 hit.
[Graphical view]
SMARTSM00292. BRCT. 1 hit.
SM00717. SANT. 1 hit.
[Graphical view]
SUPFAMSSF46689. SSF46689. 2 hits.
SSF52113. SSF52113. 1 hit.
PROSITEPS50172. BRCT. 1 hit.
PS51294. HTH_MYB. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP11938.
NextBio979511.

Entry information

Entry nameRAP1_YEAST
AccessionPrimary (citable) accession number: P11938
Secondary accession number(s): D6W0X4
Entry history
Integrated into UniProtKB/Swiss-Prot: October 1, 1989
Last sequence update: February 1, 1995
Last modified: April 16, 2014
This is version 152 of the entry and version 2 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Relevant documents

Yeast chromosome XIV

Yeast (Saccharomyces cerevisiae) chromosome XIV: 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