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P11938

- RAP1_YEAST

UniProt

P11938 - RAP1_YEAST

Protein

DNA-binding protein RAP1

Gene

RAP1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 155 (01 Oct 2014)
      Sequence version 2 (01 Feb 1995)
      Previous versions | rss
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    Functioni

    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.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi388 – 41124H-T-H motifPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. core promoter proximal region sequence-specific DNA binding Source: SGD
    2. DNA binding, bending Source: SGD
    3. G-quadruplex DNA binding Source: SGD
    4. nucleosomal DNA binding Source: SGD
    5. protein binding Source: IntAct
    6. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity Source: SGD
    7. RNA polymerase II transcription factor binding transcription factor activity Source: SGD
    8. TBP-class protein binding RNA polymerase II transcription factor activity Source: SGD
    9. telomeric DNA binding Source: SGD
    10. TFIID-class transcription factor binding Source: SGD

    GO - Biological processi

    1. chromatin silencing at silent mating-type cassette Source: SGD
    2. chromatin silencing at telomere Source: SGD
    3. establishment of chromatin silencing at telomere Source: SGD
    4. establishment of protein localization to chromatin Source: SGD
    5. establishment of protein localization to telomere Source: SGD
    6. negative regulation of chromatin silencing Source: SGD
    7. negative regulation of transcription from RNA polymerase II promoter Source: SGD
    8. positive regulation of transcription from RNA polymerase II promoter Source: SGD
    9. protection from non-homologous end joining at telomere Source: SGD
    10. regulation of glycolytic by positive regulation of transcription from RNA polymerase II promoter Source: SGD
    11. regulation of transcription by chromatin organization Source: SGD
    12. telomere maintenance Source: SGD
    13. telomere maintenance via telomere lengthening Source: SGD
    14. transcription from RNA polymerase II promoter Source: GOC

    Keywords - Molecular functioni

    Activator, Repressor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33222-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA-binding protein RAP1
    Alternative name(s):
    Repressor/activator site-binding protein
    SBF-E
    TUF
    Gene namesi
    Name:RAP1
    Synonyms:GRF1, TUF1
    Ordered Locus Names:YNL216W
    ORF Names:N1310
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XIV

    Organism-specific databases

    CYGDiYNL216w.
    SGDiS000005160. RAP1.

    Subcellular locationi

    GO - Cellular componenti

    1. cytosol Source: SGD
    2. nuclear chromosome Source: SGD
    3. nuclear chromosome, telomeric region Source: SGD
    4. nucleus Source: SGD
    5. telosome Source: SGD

    Keywords - Cellular componenti

    Chromosome, Nucleus, Telomere

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 827827DNA-binding protein RAP1PRO_0000197112Add
    BLAST

    Amino acid modifications

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Modified residuei486 – 4861Phosphothreonine1 Publication
    Modified residuei731 – 7311Phosphoserine1 Publication

    Keywords - PTMi

    Phosphoprotein

    Proteomic databases

    MaxQBiP11938.
    PaxDbiP11938.
    PeptideAtlasiP11938.

    Expressioni

    Gene expression databases

    GenevestigatoriP11938.

    Interactioni

    Subunit structurei

    RIF1, SIR3 and SIR4 associate with RAP1 C-terminus in vivo. Interacts with a GCR1 homodimer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    ESA1Q086496EBI-14821,EBI-6648
    GCN4P030695EBI-14821,EBI-7450
    RIF1P295393EBI-14821,EBI-2083307
    RIF2Q062086EBI-14821,EBI-15199
    SIR3P067012EBI-14821,EBI-17230
    SIR4P119784EBI-14821,EBI-17237

    Protein-protein interaction databases

    BioGridi35620. 277 interactions.
    DIPiDIP-851N.
    IntActiP11938. 46 interactions.
    MINTiMINT-551528.
    STRINGi4932.YNL216W.

    Structurei

    Secondary structure

    1
    827
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi365 – 37612
    Helixi379 – 3813
    Helixi386 – 3916
    Turni392 – 3943
    Helixi400 – 40910
    Helixi412 – 4143
    Beta strandi437 – 4404
    Helixi451 – 47020
    Beta strandi474 – 4763
    Beta strandi509 – 5113
    Helixi525 – 5328
    Turni533 – 5353
    Helixi538 – 54710
    Helixi549 – 5524
    Helixi554 – 5629
    Turni595 – 5973
    Helixi681 – 6844
    Helixi688 – 6903
    Turni700 – 7023
    Helixi705 – 7084
    Helixi713 – 72412
    Turni730 – 7323
    Helixi733 – 74412
    Helixi748 – 75710
    Turni758 – 7603
    Helixi762 – 7643
    Helixi765 – 77511
    Beta strandi781 – 7833
    Helixi789 – 7968
    Helixi800 – 81011
    Helixi812 – 82312

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    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[»]
    DisProtiDP00020.
    ProteinModelPortaliP11938.
    SMRiP11938. Positions 116-212, 360-601, 676-827.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP11938.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini121 – 20888BRCTPROSITE-ProRule annotationAdd
    BLAST
    Domaini355 – 41561HTH myb-typePROSITE-ProRule annotationAdd
    BLAST

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni630 – 69566Activation domainAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi71 – 744Poly-Asp
    Compositional biasi81 – 844Poly-Thr
    Compositional biasi313 – 3208Poly-Asn
    Compositional biasi614 – 62714Poly-AlaAdd
    BLAST

    Sequence similaritiesi

    Belongs to the RAP1 family.Curated
    Contains 1 BRCT domain.PROSITE-ProRule annotation
    Contains 1 HTH myb-type DNA-binding domain.PROSITE-ProRule annotation

    Phylogenomic databases

    eggNOGiNOG46211.
    HOGENOMiHOG000115833.
    KOiK09426.
    OMAiIAREFFK.
    OrthoDBiEOG74J9HM.

    Family and domain databases

    Gene3Di1.10.10.60. 3 hits.
    3.40.50.10190. 1 hit.
    InterProiIPR001357. BRCT_dom.
    IPR009057. Homeodomain-like.
    IPR017930. Myb_dom.
    IPR021661. Rap1_C.
    IPR015280. Rap1_DNA-bd.
    IPR001005. SANT/Myb.
    [Graphical view]
    PfamiPF00249. Myb_DNA-binding. 1 hit.
    PF09197. Rap1-DNA-bind. 1 hit.
    PF11626. Rap1_C. 1 hit.
    [Graphical view]
    SMARTiSM00292. BRCT. 1 hit.
    SM00717. SANT. 1 hit.
    [Graphical view]
    SUPFAMiSSF46689. SSF46689. 2 hits.
    SSF52113. SSF52113. 1 hit.
    PROSITEiPS50172. BRCT. 1 hit.
    PS51294. HTH_MYB. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P11938-1 [UniParc]FASTAAdd to Basket

    « Hide

    MSSPDDFETA PAEYVDALDP SMVVVDSGSA AVTAPSDSAA EVKANQNEEN    50
    TGATAAETSE KVDQTEVEKK DDDDTTEVGV TTTTPSIADT AATANIASTS 100
    GASVTEPTTD DTAADEKKEQ VSGPPLSNMK FYLNRDADAH DSLNDIDQLA 150
    RLIRANGGEV LDSKPRESKE NVFIVSPYNH TNLPTVTPTY IKACCQSNSL 200
    LNMENYLVPY DNFREVVDSR LQEESHSNGV DNSNSNSDNK DSIRPKTEII 250
    STNTNGATED STSEKVMVDA EQQARLQEQA QLLRQHVSST ASITSGGHND 300
    LVQIEQPQKD TSNNNNSNVN DEDNDLLTQD NNPQTADEGN ASFQAQRSMI 350
    SRGALPSHNK ASFTDEEDEF ILDVVRKNPT RRTTHTLYDE ISHYVPNHTG 400
    NSIRHRFRVY LSKRLEYVYE VDKFGKLVRD DDGNLIKTKV LPPSIKRKFS 450
    ADEDYTLAIA VKKQFYRDLF QIDPDTGRSL ITDEDTPTAI ARRNMTMDPN 500
    HVPGSEPNFA AYRTQSRRGP IAREFFKHFA EEHAAHTENA WRDRFRKFLL 550
    AYGIDDYISY YEAEKAQNRE PEPMKNLTNR PKRPGVPTPG NYNSAAKRAR 600
    NYSSQRNVQP TANAASANAA AAAAAAASNS YAIPENELLD EDTMNFISSL 650
    KNDLSNISNS LPFEYPHEIA EAIRSDFSNE DIYDNIDPDT ISFPPKIATT 700
    DLFLPLFFHF GSTRQFMDKL HEVISGDYEP SQAEKLVQDL CDETGIRKNF 750
    STSILTCLSG DLMVFPRYFL NMFKDNVNPP PNVPGIWTHD DDESLKSNDQ 800
    EQIRKLVKKH GTGRMEMRKR FFEKDLL 827
    Length:827
    Mass (Da):92,413
    Last modified:February 1, 1995 - v2
    Checksum:i67C4AFB03B3C0713
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti672 – 6721A → R in AAA18404. (PubMed:3315231)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M18068 Unassigned DNA. Translation: AAA18404.1.
    X78898 Genomic DNA. Translation: CAA55491.1.
    Z71492 Genomic DNA. Translation: CAA96118.1.
    BK006947 Genomic DNA. Translation: DAA10340.1.
    PIRiS50714.
    RefSeqiNP_014183.1. NM_001183054.1.

    Genome annotation databases

    EnsemblFungiiYNL216W; YNL216W; YNL216W.
    GeneIDi855505.
    KEGGisce:YNL216W.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    M18068 Unassigned DNA. Translation: AAA18404.1 .
    X78898 Genomic DNA. Translation: CAA55491.1 .
    Z71492 Genomic DNA. Translation: CAA96118.1 .
    BK006947 Genomic DNA. Translation: DAA10340.1 .
    PIRi S50714.
    RefSeqi NP_014183.1. NM_001183054.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1IGN X-ray 2.25 A/B 353-598 [» ]
    2L42 NMR - A 116-212 [» ]
    3CZ6 X-ray 1.85 A/B 672-827 [» ]
    3OWT X-ray 2.00 A/B 672-827 [» ]
    3UKG X-ray 2.95 A 360-601 [» ]
    4BJ5 X-ray 3.29 C/E 627-827 [» ]
    4BJ6 X-ray 3.26 C/E 627-827 [» ]
    4BJT X-ray 1.61 A/B/C 627-827 [» ]
    4GFB X-ray 2.99 A 358-602 [» ]
    DisProti DP00020.
    ProteinModelPortali P11938.
    SMRi P11938. Positions 116-212, 360-601, 676-827.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 35620. 277 interactions.
    DIPi DIP-851N.
    IntActi P11938. 46 interactions.
    MINTi MINT-551528.
    STRINGi 4932.YNL216W.

    Proteomic databases

    MaxQBi P11938.
    PaxDbi P11938.
    PeptideAtlasi P11938.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YNL216W ; YNL216W ; YNL216W .
    GeneIDi 855505.
    KEGGi sce:YNL216W.

    Organism-specific databases

    CYGDi YNL216w.
    SGDi S000005160. RAP1.

    Phylogenomic databases

    eggNOGi NOG46211.
    HOGENOMi HOG000115833.
    KOi K09426.
    OMAi IAREFFK.
    OrthoDBi EOG74J9HM.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33222-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P11938.
    NextBioi 979511.

    Gene expression databases

    Genevestigatori P11938.

    Family and domain databases

    Gene3Di 1.10.10.60. 3 hits.
    3.40.50.10190. 1 hit.
    InterProi IPR001357. BRCT_dom.
    IPR009057. Homeodomain-like.
    IPR017930. Myb_dom.
    IPR021661. Rap1_C.
    IPR015280. Rap1_DNA-bd.
    IPR001005. SANT/Myb.
    [Graphical view ]
    Pfami PF00249. Myb_DNA-binding. 1 hit.
    PF09197. Rap1-DNA-bind. 1 hit.
    PF11626. Rap1_C. 1 hit.
    [Graphical view ]
    SMARTi SM00292. BRCT. 1 hit.
    SM00717. SANT. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46689. SSF46689. 2 hits.
    SSF52113. SSF52113. 1 hit.
    PROSITEi PS50172. BRCT. 1 hit.
    PS51294. HTH_MYB. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    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.
      , 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. 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. 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.

    Entry informationi

    Entry nameiRAP1_YEAST
    AccessioniPrimary (citable) accession number: P11938
    Secondary accession number(s): D6W0X4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1989
    Last sequence update: February 1, 1995
    Last modified: October 1, 2014
    This is version 155 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Miscellaneous

    Present with 4390 molecules/cell in log phase SD medium.1 Publication

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome XIV
      Yeast (Saccharomyces cerevisiae) chromosome XIV: entries and gene names

    External Data

    Dasty 3