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P01123 (YPT1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Last modified April 16, 2014. Version 161. 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:
GTP-binding protein YPT1
Alternative name(s):
Protein YP2
Rab GTPase YPT1
Transport GTPase YPT1
Gene names
Name:YPT1
Synonyms:YP2
Ordered Locus Names:YFL038C
OrganismSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) [Reference proteome]
Taxonomic identifier559292 [NCBI]
Taxonomic lineageEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces

Protein attributes

Sequence length206 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Involved in the trafficking of secretory vesicles from the endoplasmic reticulum (ER) to the Golgi. Regulates correct targeting and tethering of vesicles to target membranes by catalyzing the selective recruitment of proteins required for tethering and fusion onto membranes. Vesicular transport depends on shuttling of YPT1 between membrane and cytosol by GDI1, probably by recycling it to its membrane of origin after a vesicle fusion event. Required for sorting and transport of proteins from the ER through the Golgi compartment. Also involved in the recycling of membrane proteins. Ref.8 Ref.14 Ref.18 Ref.20 Ref.21 Ref.22

Enzyme regulation

Alternates between an inactive form bound to GDP and an active form bound to GTP. Activated by the guanine nucleotide-exchange factors (GEFs) DSS4 and TRAPP complex, and inactivated by GTPase-activating proteins (GAPs) GYP1, GYP5 and GYP8. Ref.13 Ref.15 Ref.16 Ref.20

Subunit structure

Forms a complex with the Rab escort protein (REP) MRS6, which is recognized by Rab geranylgeranyltransferase BET2-BET4. Interacts with the Rab GDP dissociation inhibitor GDI1, which can retrieve from and deliver to membranes the GDP-bound and prenylated form of YPT1. Interacts with YIP1, which is required for proper membrane targeting of prenylated YPT1. Interacts with YIF1, YIP3, YIP4 and YIP5. Ref.11 Ref.17 Ref.19 Ref.21

Subcellular location

Endoplasmic reticulum membrane; Peripheral membrane protein. Golgi apparatus membrane; Peripheral membrane protein. Cytoplasm. Note: ER and Golgi when GTP-bound. Cytoplasmic when bound to GDI1. Ref.21

Post-translational modification

Prenylation is required for interaction with GDI1 and YIP1.

Sequence similarities

Belongs to the small GTPase superfamily. Rab family.

Caution

In Ref.7 the location of any palmitoylation was not determined. Mutagenesis of either Cys-205 or Cys-206 would disrupt normal geranylgeranylation, and there would be no primary membrane association for secondary S-palmitoylation to occur at some other position, for example Cys-23. Mutagenesis of both Cys-205 and Cys-206 is lethal, so protein production could not have been observed.

Ontologies

Keywords
   Biological processER-Golgi transport
Protein transport
Transport
   Cellular componentCytoplasm
Endoplasmic reticulum
Golgi apparatus
Membrane
   LigandGTP-binding
Nucleotide-binding
   PTMAcetylation
Lipoprotein
Phosphoprotein
Prenylation
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processCOPII-coated vesicle budding

Inferred from mutant phenotype PubMed 15689495. Source: SGD

CVT pathway

Inferred from mutant phenotype PubMed 20375281. Source: SGD

ER to Golgi vesicle-mediated transport

Inferred from mutant phenotype PubMed 15689495PubMed 2504726Ref.10. Source: SGD

GTP catabolic process

Inferred from direct assay Ref.6Ref.12. Source: GOC

Golgi vesicle budding

Inferred from genetic interaction PubMed 18388317. Source: SGD

Golgi vesicle docking

Inferred from mutant phenotype PubMed 9545229. Source: SGD

SNARE complex disassembly

Inferred from mutant phenotype PubMed 9157884. Source: SGD

early endosome to Golgi transport

Inferred from mutant phenotype PubMed 20059749. Source: SGD

endocytic recycling

Inferred from mutant phenotype PubMed 20059749. Source: SGD

macroautophagy

Inferred from mutant phenotype PubMed 20375281. Source: SGD

pre-mRNA catabolic process

Inferred from mutant phenotype PubMed 22844259. Source: SGD

protein complex assembly

Inferred from direct assay PubMed 8603910. Source: SGD

regulation of endoplasmic reticulum unfolded protein response

Inferred from mutant phenotype PubMed 22844259. Source: SGD

retrograde vesicle-mediated transport, Golgi to ER

Inferred from mutant phenotype PubMed 18388317. Source: SGD

small GTPase mediated signal transduction

Inferred from electronic annotation. Source: InterPro

   Cellular_componentGolgi membrane

Inferred from direct assay PubMed 10747087. Source: SGD

Golgi stack

Inferred from direct assay Ref.21. Source: SGD

cytoplasmic vesicle

Inferred from direct assay PubMed 23129774. Source: SGD

endoplasmic reticulum membrane

Inferred from direct assay PubMed 10747087. Source: SGD

pre-autophagosomal structure

Inferred from direct assay PubMed 20375281. Source: SGD

trans-Golgi network

Inferred from direct assay PubMed 20059749. Source: SGD

   Molecular_functionGTP binding

Inferred from electronic annotation. Source: UniProtKB-KW

GTPase activity

Inferred from direct assay Ref.6Ref.12. Source: SGD

SNARE binding

Inferred from direct assay PubMed 18388317. Source: SGD

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 206206GTP-binding protein YPT1
PRO_0000121318

Regions

Nucleotide binding15 – 228GTP By similarity
Nucleotide binding63 – 675GTP By similarity
Nucleotide binding121 – 1244GTP By similarity
Region63 – 8018Interaction with GDI1
Region189 – 1957Interaction with GDI1
Motif37 – 459Effector region Probable

Amino acid modifications

Modified residue11N-acetylmethionine Ref.5
Modified residue1721Phosphoserine Ref.24
Modified residue1741Phosphoserine Ref.23
Lipidation2051S-geranylgeranyl cysteine Ref.14
Lipidation2061S-geranylgeranyl cysteine Ref.14

Experimental info

Mutagenesis171S → G: Decreases GTP binding and increases GTP hydrolysis. Ref.6
Mutagenesis211K → M: Abolishes GTP binding. Ref.6
Mutagenesis371Y → F: No change. Ref.9
Mutagenesis391S → A: No change. Ref.9
Mutagenesis401T → S: No change. Ref.9
Mutagenesis411I → M: Lethal. Ref.9
Mutagenesis431V → E: No change. Ref.9
Mutagenesis441D → N: Temperature-sensitive phenotype. Ref.9
Mutagenesis651A → T: Decreases GTP binding and GTP hydrolysis. Ref.6
Mutagenesis671Q → L: Locks YPT1 in the GTP-bound form by reducing GTP hydrolysis rate 40-fold. Ref.12 Ref.22
Mutagenesis1211N → I: Abolishes GTP binding. Ref.6
Mutagenesis1361A → D: Loss of function at 37 degrees Celsius. Ref.9 Ref.10
Mutagenesis2051C → S: Abolishes membrane association. Lethal; when associated with S-206. Ref.7 Ref.14
Mutagenesis2061C → S: Abolishes membrane association. Lethal; when associated with S-205. Ref.7 Ref.14
Sequence conflict1711E → Q in CAA25036. Ref.1

Secondary structure

................................. 206
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P01123 [UniParc].

Last modified November 1, 1995. Version 2.
Checksum: F8C704F6BF2D227B

FASTA20623,214
        10         20         30         40         50         60 
MNSEYDYLFK LLLIGNSGVG KSCLLLRFSD DTYTNDYIST IGVDFKIKTV ELDGKTVKLQ 

        70         80         90        100        110        120 
IWDTAGQERF RTITSSYYRG SHGIIIVYDV TDQESFNGVK MWLQEIDRYA TSTVLKLLVG 

       130        140        150        160        170        180 
NKCDLKDKRV VEYDVAKEFA DANKMPFLET SALDSTNVED AFLTMARQIK ESMSQQNLNE 

       190        200 
TTQKKEDKGN VNLKGQSLTN TGGGCC 

« Hide

References

« Hide 'large scale' references
[1]"A yeast gene encoding a protein homologous to the human c-has/bas proto-oncogene product."
Gallwitz D., Donath C., Sander C.
Nature 306:704-707(1983) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Analysis of the nucleotide sequence of chromosome VI from Saccharomyces cerevisiae."
Murakami Y., Naitou M., Hagiwara H., Shibata T., Ozawa M., Sasanuma S., Sasanuma M., Tsuchiya Y., Soeda E., Yokoyama K., Yamazaki M., Tashiro H., Eki T.
Nat. Genet. 10:261-268(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[3]Saccharomyces Genome Database
Submitted (DEC-2009) to the EMBL/GenBank/DDBJ databases
Cited for: GENOME REANNOTATION.
Strain: ATCC 204508 / S288c.
[4]"Approaching a complete repository of sequence-verified protein-encoding clones for Saccharomyces cerevisiae."
Hu Y., Rolfs A., Bhullar B., Murthy T.V.S., Zhu C., Berger M.F., Camargo A.A., Kelley F., McCarron S., Jepson D., Richardson A., Raphael J., Moreira D., Taycher E., Zuo D., Mohr S., Kane M.F., Williamson J. expand/collapse author list , Simpson A.J.G., Bulyk M.L., Harlow E., Marsischky G., Kolodner R.D., LaBaer J.
Genome Res. 17:536-543(2007) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: ATCC 204508 / S288c.
[5]Bienvenut W.V., Peters C.
Submitted (MAY-2005) to UniProtKB
Cited for: PROTEIN SEQUENCE OF 1-46; 49-55; 59-69; 72-79; 101-116 AND 130-167, CLEAVAGE OF INITIATOR METHIONINE, ACETYLATION AT MET-1, IDENTIFICATION BY MASS SPECTROMETRY.
[6]"Biochemical properties of the ras-related YPT protein in yeast: a mutational analysis."
Wagner P., Molenaar C.M.T., Rauh A.J.G., Broekel R., Schmitt H.D., Gallwitz D.
EMBO J. 6:2373-2379(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF SER-17; LYS-21; ALA-65 AND ASN-121.
[7]"A carboxyl-terminal cysteine residue is required for palmitic acid binding and biological activity of the ras-related yeast YPT1 protein."
Molenaar C.M.T., Prange R., Gallwitz D.
EMBO J. 7:971-976(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: PALMITOYLATION, MUTAGENESIS OF CYS-205 AND CYS-206.
[8]"Study of a temperature-sensitive mutant of the ras-related YPT1 gene product in yeast suggests a role in the regulation of intracellular calcium."
Schmitt H.D., Puzicha M., Gallwitz D.
Cell 53:635-647(1988) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS, POSSIBLE FUNCTION.
[9]"Mutational analysis of the putative effector domain of the GTP-binding Ypt1 protein in yeast suggests specific regulation by a novel GAP activity."
Becker J., Tan T.J., Trepte H.-H., Gallwitz D.
EMBO J. 10:785-792(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF TYR-37; SER-39; THR-40; ILE-41; VAL-43 AND ASP-44.
[10]"The Ypt1 GTPase is essential for the first two steps of the yeast secretory pathway."
Jedd G., Richardson C.J., Litt R.J., Segev N.
J. Cell Biol. 131:583-590(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF ALA-136.
[11]"Amino- and carboxy-terminal domains of the yeast Rab escort protein are both required for binding of Ypt small G proteins."
Bauer B.E., Lorenzetti S., Miaczynska M., Bui D.M., Schweyen R.J., Ragnini A.
Mol. Biol. Cell 7:1521-1533(1996) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH MRS6.
[12]"GTP hydrolysis is not important for Ypt1 GTPase function in vesicular transport."
Richardson C.J., Jones S., Litt R.J., Segev N.
Mol. Cell. Biol. 18:827-838(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: MUTAGENESIS OF GLN-67.
[13]"Distinct subclasses of small GTPases interact with guanine nucleotide exchange factors in a similar manner."
Day G.-J., Mosteller R.D., Broek D.
Mol. Cell. Biol. 18:7444-7454(1998) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION.
[14]"Functional implications of genetic interactions between genes encoding small GTPases involved in vesicular transport in yeast."
Yoo J.S., Grabowski R., Xing L., Trepte H.H., Schmitt H.D., Gallwitz D.
Mol. Gen. Genet. 261:80-91(1999)
Cited for: ISOPRENYLATION, MUTAGENESIS OF CYS-205 AND CYS-206, FUNCTION.
[15]"The TRAPP complex is a nucleotide exchanger for Ypt1 and Ypt31/32."
Jones S., Newman C., Liu F., Segev N.
Mol. Biol. Cell 11:4403-4411(2000) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION.
[16]"Yeast rab GTPase-activating protein Gyp1p localizes to the Golgi apparatus and is a negative regulator of Ypt1p."
Du L.-L., Novick P.
Mol. Biol. Cell 12:1215-1226(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: ENZYME REGULATION.
[17]"Saccharomyces cerevisiae Pra1p/Yip3p interacts with Yip1p and Rab proteins."
Calero M., Collins R.N.
Biochem. Biophys. Res. Commun. 290:676-681(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH YIP3.
[18]"The Rab GTPase Ypt1p and tethering factors couple protein sorting at the ER to vesicle targeting to the Golgi apparatus."
Morsomme P., Riezman H.
Dev. Cell 2:307-317(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION.
[19]"Identification of the novel proteins Yip4p and Yip5p as Rab GTPase interacting factors."
Calero M., Winand N.J., Collins R.N.
FEBS Lett. 515:89-98(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: INTERACTION WITH YIF1; YIP4 AND YIP5.
[20]"Significance of GTP hydrolysis in Ypt1p-regulated endoplasmic reticulum to Golgi transport revealed by the analysis of two novel Ypt1-GAPs."
De Antoni A., Schmitzova J., Trepte H.-H., Gallwitz D., Albert S.
J. Biol. Chem. 277:41023-41031(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, ENZYME REGULATION.
[21]"Dual prenylation is required for Rab protein localization and function."
Calero M., Chen C.Z., Zhu W., Winand N.J., Havas K.A., Gilbert P.M., Burd C.G., Collins R.N.
Mol. Biol. Cell 14:1852-1867(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, INTERACTION WITH YIP1, SUBCELLULAR LOCATION.
[22]"The GTPase-activating enzyme Gyp1p is required for recycling of internalized membrane material by inactivation of the Rab/Ypt GTPase Ypt1p."
Lafourcade C., Galan J.-M., Gloor Y., Haguenauer-Tsapis R., Peter M.
Mol. Cell. Biol. 24:3815-3826(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, MUTAGENESIS OF GLN-67.
[23]"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-174, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[24]"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: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-172, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[25]"Sites of ubiquitin attachment in Saccharomyces cerevisiae."
Starita L.M., Lo R.S., Eng J.K., von Haller P.D., Fields S.
Proteomics 12:236-240(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
[26]"Structure of Rab GDP-dissociation inhibitor in complex with prenylated YPT1 GTPase."
Rak A., Pylypenko O., Durek T., Watzke A., Kushnir S., Brunsveld L., Waldmann H., Goody R.S., Alexandrov K.
Science 302:646-650(2003) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH GDI1.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X00209 Genomic DNA. Translation: CAA25036.1.
D50617 Genomic DNA. Translation: BAA09201.1.
AY558467 Genomic DNA. Translation: AAS56793.1.
BK006940 Genomic DNA. Translation: DAA12402.1.
PIRTVBYQ2. S56216.
RefSeqNP_116615.1. NM_001179928.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1UKVX-ray1.50Y1-206[»]
1YZNX-ray2.06A3-172[»]
2BCGX-ray1.48Y1-206[»]
3CUEX-ray3.70F/L/R/X1-206[»]
ProteinModelPortalP01123.
SMRP01123. Positions 3-196.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

BioGrid31108. 132 interactions.
DIPDIP-2019N.
IntActP01123. 23 interactions.
MINTMINT-389361.
STRING4932.YFL038C.

Proteomic databases

PaxDbP01123.
PeptideAtlasP01123.
PRIDEP01123.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblFungiYFL038C; YFL038C; YFL038C.
GeneID850505.
KEGGsce:YFL038C.

Organism-specific databases

CYGDYFL038c.
SGDS000001856. YPT1.

Phylogenomic databases

eggNOGCOG1100.
GeneTreeENSGT00720000108592.
HOGENOMHOG000233968.
KOK07874.
OMAVESYIST.
OrthoDBEOG7BGHXR.

Enzyme and pathway databases

BioCycYEAST:G3O-30424-MONOMER.

Gene expression databases

GenevestigatorP01123.

Family and domain databases

Gene3D3.40.50.300. 1 hit.
InterProIPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]
PfamPF00071. Ras. 1 hit.
[Graphical view]
PRINTSPR00449. RASTRNSFRMNG.
SMARTSM00175. RAB. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 1 hit.
TIGRFAMsTIGR00231. small_GTP. 1 hit.
PROSITEPS51419. RAB. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

EvolutionaryTraceP01123.
NextBio966209.
PROP01123.

Entry information

Entry nameYPT1_YEAST
AccessionPrimary (citable) accession number: P01123
Secondary accession number(s): D6VTJ2
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 1, 1995
Last modified: April 16, 2014
This is version 161 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 VI

Yeast (Saccharomyces cerevisiae) chromosome VI: 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