GTP-binding protein YPT1 - Saccharomyces cerevisiae (Baker's yeast)

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Reviewed, UniProtKB/Swiss-Prot P01123 (YPT1_YEAST)

Last modified November 25, 2008. Version 106. History...

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Names and origin · Protein attributes · General annotation (Comments) · Ontologies · Binary interactions · Sequence annotation (Features) · Sequences · References · Cross-references · Entry information · Relevant documents

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Names and origin

Protein names

Recommended name:
    GTP-binding protein YPT1
Alternative name(s):
    Rab GTPase YPT1
    Transport GTPase YPT1
    Protein YP2

Gene names

Name:	YPT1
Synonyms:	YP2
Ordered Locus Names:	YFL038C

Organism

Saccharomyces cerevisiae (Baker's yeast) [Complete proteome]

Taxonomic identifier

4932 [NCBI]

Taxonomic lineage

Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces

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Protein attributes

Sequence length	206 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

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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.
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.
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.
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.
Post-translational modification	Prenylation is required for interaction with GDI1 and YIP1. Palmitoylation is required for membrane attachment and biological function.
Sequence similarities	Belongs to the small GTPase superfamily. Rab family.

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Ontologies

Keywords
Biological process	ER-Golgi transport Protein transport Transport
Cellular component	Cytoplasm Endoplasmic reticulum Golgi apparatus Membrane
Ligand	GTP-binding Nucleotide-binding
PTM	Acetylation Lipoprotein Palmitate Phosphoprotein Prenylation
Technical term	3D-structure Complete proteome Direct protein sequencing
Gene Ontology (GO)
Biological process	ER to Golgi vesicle-mediated transport Traceable author statement. Source: SGD Golgi vesicle budding Inferred from genetic interaction. Source: SGD protein complex assembly Inferred from direct assay. Source: SGD protein retention in Golgi apparatus Inferred from genetic interaction. Source: SGD protein transport Inferred from electronic annotation. Source: InterPro retrograde vesicle-mediated transport, Golgi to ER Inferred from genetic interaction. Source: SGD small GTPase mediated signal transduction Inferred from electronic annotation. Source: InterPro
Cellular component	Golgi membrane Inferred from direct assay. Source: SGD endoplasmic reticulum membrane Inferred from direct assay. Source: SGD mitochondrion Inferred from direct assay. Source: SGD
Molecular function	GTP binding Inferred from electronic annotation. Source: InterPro GTPase activity Traceable author statement. Source: SGD protein binding Ref.15 Ref.23 Inferred from physical interaction. Source: IntAct
Complete GO annotation...

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Binary interactions

With	Entry	#Exp.	IntAct
COG2	P53271	1	EBI-29496,EBI-16614
COG3	P40094	1	EBI-29496,EBI-16605
GDI1	P39958	1	EBI-29496,EBI-7517
YIP3	P53633	1	EBI-29496,EBI-25301

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Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 206

206

GTP-binding protein YPT1

PRO_0000121318

Regions

Nucleotide binding

15 – 22

GTP By similarity

Nucleotide binding

63 – 67

GTP By similarity

Nucleotide binding

121 – 124

GTP By similarity

Region

63 – 80

Interaction with GDI1

Region

189 – 195

Interaction with GDI1

Motif

37 – 45

Effector region Probable

Amino acid modifications

Modified residue

N-acetylmethionine

Modified residue

Phosphoserine

Modified residue

172

Phosphoserine

Modified residue

174

Phosphoserine

Lipidation

205

S-palmitoyl cysteine

Lipidation

206

S-geranylgeranyl cysteine

Experimental info

Mutagenesis

S → G: Decreases GTP binding and increases GTP hydrolysis

Mutagenesis

K → M: Abolishes GTP binding

Mutagenesis

Y → F: No change

Mutagenesis

S → A: No change

Mutagenesis

T → S: No change

Mutagenesis

I → M: Lethal

Mutagenesis

V → E: No change

Mutagenesis

D → N: Temperature-sensitive phenotype

Mutagenesis

A → T: Decreases GTP binding and GTP hydrolysis

Mutagenesis

Q → L: Locks YPT1 in the GTP-bound form by reducing GTP hydrolysis rate 40-fold

Mutagenesis

121

N → I: Abolishes GTP binding

Mutagenesis

136

A → D: Loss of function at 37 degrees Celsius

Mutagenesis

205

C → S: Abolishes palmitoylation and membrane association; when associated with S-206. Reduced palmitoylation level

Mutagenesis

206

C → S: Abolishes palmitoylation and membrane association; when associated with S-205. Reduced palmitoylation level

Sequence conflict

171

E → Q in CAA25036. Ref.1

Secondary structure

206

Helix Strand Turn

Details...

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Sequences

Sequence

Length

Mass (Da)

Tools

P01123-1 [UniParc].

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

206

23,214

        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

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References

	« Hide 'large scale' referencesShow '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: 6318115] [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: 7670463] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: ATCC 204511 / S288c / AB972.
[3]	"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. LaBaer J. Genome Res. 17:536-543(2007) [PubMed: 17322287] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: ATCC 204508 / S288c.
[4]	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, MASS SPECTROMETRY.
[5]	"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: 3311726] [Abstract] Cited for: MUTAGENESIS OF SER-17; LYS-21; ALA-65 AND ASN-121.
[6]	"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: 3042385] [Abstract] Cited for: PALMITOYLATION AT CYS-205 AND CYS-206, MUTAGENESIS OF CYS-205 AND CYS-206.
[7]	"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: 3286011] [Abstract] Cited for: MUTAGENESIS, POSSIBLE FUNCTION.
[8]	"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: 2009858] [Abstract] Cited for: MUTAGENESIS OF TYR-37; SER-39; THR-40; ILE-41; VAL-43 AND ASP-44.
[9]	"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: 7593181] [Abstract] Cited for: MUTAGENESIS OF ALA-136.
[10]	"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: 8898359] [Abstract] Cited for: INTERACTION WITH MRS6.
[11]	"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: 9447979] [Abstract] Cited for: MUTAGENESIS OF GLN-67.
[12]	"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: 9819430] [Abstract] Cited for: ENZYME REGULATION.
[13]	"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: 11102533] [Abstract] Cited for: ENZYME REGULATION.
[14]	"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: 11359917] [Abstract] Cited for: ENZYME REGULATION.
[15]	"Saccharomyces cerevisiae Pra1p/Yip3p interacts with Yip1p and Rab proteins." Calero M., Collins R.N. Biochem. Biophys. Res. Commun. 290:676-681(2002) [PubMed: 11785952] [Abstract] Cited for: INTERACTION WITH YIP3.
[16]	"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: 11879636] [Abstract] Cited for: FUNCTION.
[17]	"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: 11943201] [Abstract] Cited for: INTERACTION WITH YIF1; YIP4 AND YIP5.
[18]	"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: 12189143] [Abstract] Cited for: FUNCTION, ENZYME REGULATION.
[19]	"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: 12802060] [Abstract] Cited for: FUNCTION, INTERACTION WITH YIP1, SUBCELLULAR LOCATION.
[20]	"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: 15082776] [Abstract] Cited for: FUNCTION, MUTAGENESIS OF GLN-67.
[21]	"Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases." Smolka M.B., Albuquerque C.P., Chen S.H., Zhou H. Proc. Natl. Acad. Sci. U.S.A. 104:10364-10369(2007) [PubMed: 17563356] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174, MASS SPECTROMETRY.
[22]	"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: 18407956] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-17; SER-172 AND SER-174, MASS SPECTROMETRY.
[23]	"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: 14576435] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH GDI1.
+	Additional computationally mapped references.