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P11938

- RAP1_YEAST

UniProt

P11938 - RAP1_YEAST

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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

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. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity Source: SGD
  6. RNA polymerase II transcription factor binding transcription factor activity Source: SGD
  7. TBP-class protein binding RNA polymerase II transcription factor activity Source: SGD
  8. telomeric DNA binding Source: SGD
  9. 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
Complete GO annotation...

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
Complete GO annotation...

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 – 37612Combined sources
Helixi379 – 3813Combined sources
Helixi386 – 3916Combined sources
Turni392 – 3943Combined sources
Helixi400 – 40910Combined sources
Helixi412 – 4143Combined sources
Beta strandi437 – 4404Combined sources
Helixi451 – 47020Combined sources
Beta strandi474 – 4763Combined sources
Beta strandi509 – 5113Combined sources
Helixi525 – 5328Combined sources
Turni533 – 5353Combined sources
Helixi538 – 54710Combined sources
Helixi549 – 5524Combined sources
Helixi554 – 5629Combined sources
Turni595 – 5973Combined sources
Helixi681 – 6844Combined sources
Helixi688 – 6903Combined sources
Turni700 – 7023Combined sources
Helixi705 – 7084Combined sources
Helixi713 – 72412Combined sources
Turni730 – 7323Combined sources
Helixi733 – 74412Combined sources
Helixi748 – 75710Combined sources
Turni758 – 7603Combined sources
Helixi762 – 7643Combined sources
Helixi765 – 77511Combined sources
Beta strandi781 – 7833Combined sources
Helixi789 – 7968Combined sources
Helixi800 – 81011Combined sources
Helixi812 – 82312Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiP11938.
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

        10         20         30         40         50
MSSPDDFETA PAEYVDALDP SMVVVDSGSA AVTAPSDSAA EVKANQNEEN
60 70 80 90 100
TGATAAETSE KVDQTEVEKK DDDDTTEVGV TTTTPSIADT AATANIASTS
110 120 130 140 150
GASVTEPTTD DTAADEKKEQ VSGPPLSNMK FYLNRDADAH DSLNDIDQLA
160 170 180 190 200
RLIRANGGEV LDSKPRESKE NVFIVSPYNH TNLPTVTPTY IKACCQSNSL
210 220 230 240 250
LNMENYLVPY DNFREVVDSR LQEESHSNGV DNSNSNSDNK DSIRPKTEII
260 270 280 290 300
STNTNGATED STSEKVMVDA EQQARLQEQA QLLRQHVSST ASITSGGHND
310 320 330 340 350
LVQIEQPQKD TSNNNNSNVN DEDNDLLTQD NNPQTADEGN ASFQAQRSMI
360 370 380 390 400
SRGALPSHNK ASFTDEEDEF ILDVVRKNPT RRTTHTLYDE ISHYVPNHTG
410 420 430 440 450
NSIRHRFRVY LSKRLEYVYE VDKFGKLVRD DDGNLIKTKV LPPSIKRKFS
460 470 480 490 500
ADEDYTLAIA VKKQFYRDLF QIDPDTGRSL ITDEDTPTAI ARRNMTMDPN
510 520 530 540 550
HVPGSEPNFA AYRTQSRRGP IAREFFKHFA EEHAAHTENA WRDRFRKFLL
560 570 580 590 600
AYGIDDYISY YEAEKAQNRE PEPMKNLTNR PKRPGVPTPG NYNSAAKRAR
610 620 630 640 650
NYSSQRNVQP TANAASANAA AAAAAAASNS YAIPENELLD EDTMNFISSL
660 670 680 690 700
KNDLSNISNS LPFEYPHEIA EAIRSDFSNE DIYDNIDPDT ISFPPKIATT
710 720 730 740 750
DLFLPLFFHF GSTRQFMDKL HEVISGDYEP SQAEKLVQDL CDETGIRKNF
760 770 780 790 800
STSILTCLSG DLMVFPRYFL NMFKDNVNPP PNVPGIWTHD DDESLKSNDQ
810 820
EQIRKLVKKH GTGRMEMRKR FFEKDLL
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:
EMBLi
GenBanki
DDBJi
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:
EMBLi
GenBanki
DDBJi
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:
PDBei
RCSB PDBi
PDBji
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.
InParanoidi P11938.
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

« Hide 'large scale' publications
  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: November 26, 2014
This is version 157 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