P11938 (RAP1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

Organism

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]

Taxonomic identifier

559292 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Fungi › Dikarya › Ascomycota › saccharomyceta › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › Saccharomyces cerevisiae

Protein attributes

Sequence length	827 AA.
Sequence status	Complete.
Protein existence	Evidence 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. Chromosome › telomere.
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 process	Transcription Transcription regulation
Cellular component	Chromosome Nucleus Telomere
Ligand	DNA-binding
Molecular function	Activator Repressor
PTM	Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	chromatin silencing at silent mating-type cassette 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 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 via telomere lengthening Inferred from direct assay PubMed 9020083. Source: SGD
Cellular_component	cytosol Inferred from direct assay PubMed 22932476. Source: SGD nuclear nucleosome Inferred from direct assay PubMed 19782036. Source: SGD nuclear telomere cap complex Inferred from direct assay PubMed 9710643. Source: SGD
Molecular_function	DNA 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 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...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
ESA1	Q08649	6	EBI-14821,EBI-6648
GCN4	P03069	5	EBI-14821,EBI-7450
SIR3	P06701	2	EBI-14821,EBI-17230
SIR4	P11978	2	EBI-14821,EBI-17237

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 827

827

DNA-binding protein RAP1

PRO_0000197112

Regions

Domain

121 – 208

88

BRCT

Domain

355 – 415

61

HTH myb-type

DNA binding

388 – 411

24

H-T-H motif

Region

630 – 695

66

Activation domain

Compositional bias

71 – 74

4

Poly-Asp

Compositional bias

81 – 84

4

Poly-Thr

Compositional bias

313 – 320

8

Poly-Asn

Compositional bias

614 – 627

14

Poly-Ala

Amino acid modifications

Modified residue

486

1

Phosphothreonine Ref.8

Modified residue

731

1

Phosphoserine Ref.9

Experimental info

Sequence conflict

672

1

A → R in AAA18404. Ref.1

Secondary structure

1

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827

Helix Strand Turn

Details...

Helix

365 – 376

12

Helix

379 – 381

3

Helix

386 – 391

6

Turn

392 – 394

3

Helix

400 – 409

10

Helix

412 – 414

3

Beta strand

437 – 440

4

Helix

451 – 470

20

Beta strand

474 – 476

3

Beta strand

509 – 511

3

Helix

525 – 532

8

Turn

533 – 535

3

Helix

538 – 547

10

Helix

549 – 552

4

Helix

554 – 562

9

Turn

595 – 597

3

Helix

681 – 684

4

Helix

688 – 690

3

Turn

700 – 702

3

Helix

705 – 708

4

Helix

713 – 724

12

Turn

730 – 732

3

Helix

733 – 744

12

Helix

748 – 757

10

Turn

758 – 760

3

Helix

762 – 764

3

Helix

765 – 775

11

Beta strand

781 – 783

3

Helix

789 – 796

8

Helix

800 – 810

11

Helix

812 – 823

12

Sequences

	Sequence		Length	Mass (Da)
	P11938 [UniParc]. Last modified February 1, 1995. Version 2. Checksum: 67C4AFB03B3C0713	FASTA	827	92,413
	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

References

	« Hide 'large scale' referencesShow '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. , 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 96604 / S288c / FY1679.
[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, MASS SPECTROMETRY. 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, MASS SPECTROMETRY.
[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.

PIR

S50714.

RefSeq

NP_014183.1. NM_001183054.1.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]

DisProt

DP00020.

ProteinModelPortal

P11938.

SMR

P11938. Positions 116-212, 360-601, 676-827.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-851N.

IntAct

P11938. 43 interactions.

MINT

MINT-551528.

STRING

4932.YNL216W.

Proteomic databases

PaxDb

P11938.

PeptideAtlas

P11938.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YNL216W; YNL216W; YNL216W.

GeneID

855505.

KEGG

sce:YNL216W.

Organism-specific databases

CYGD

YNL216w.

SGD

S000005160. RAP1.

Phylogenomic databases

eggNOG

NOG46211.

HOGENOM

HOG000115833.

KO

K09426.

OMA

IAREFFK.

OrthoDB

EOG74J9HM.

Enzyme and pathway databases

BioCyc

YEAST:G3O-33222-MONOMER.

Gene expression databases

Genevestigator

P11938.

Family and domain databases

Gene3D

1.10.10.60. 3 hits.
3.40.50.10190. 1 hit.

InterPro

IPR001357. BRCT_dom.
IPR009057. Homeodomain-like.
IPR017930. Myb_dom.
IPR021661. Rap1_C.
IPR015280. Rap1_DNA-bd.
IPR001005. SANT/Myb.
[Graphical view]

Pfam

PF00249. Myb_DNA-binding. 1 hit.
PF09197. Rap1-DNA-bind. 1 hit.
PF11626. Rap1_C. 1 hit.
[Graphical view]

SMART

SM00292. BRCT. 1 hit.
SM00717. SANT. 1 hit.
[Graphical view]

SUPFAM

SSF46689. SSF46689. 2 hits.
SSF52113. SSF52113. 1 hit.

PROSITE

PS50172. BRCT. 1 hit.
PS51294. HTH_MYB. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P11938.

NextBio

979511.

Entry information

Entry name

RAP1_YEAST

Accession

Primary (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:	November 13, 2013
This is version 147 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program