P01123 (YPT1_YEAST) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended 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

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	206 AA.
Sequence status	Complete.
Protein existence	Evidence 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 process	ER-Golgi transport Protein transport Transport
Cellular component	Cytoplasm Endoplasmic reticulum Golgi apparatus Membrane
Ligand	GTP-binding Nucleotide-binding
PTM	Acetylation Lipoprotein Phosphoprotein Prenylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	COPII-coated vesicle budding Inferred from mutant phenotype PubMed 15689495. Source: SGD CVT pathway Inferred from mutant phenotype PubMed 20375281. Source: SGD 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 protein complex assembly Inferred from direct assay PubMed 8603910. 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_component	Golgi membrane Inferred from direct assay PubMed 10747087. Source: SGD Golgi stack Inferred from direct assay Ref.21. Source: SGD endoplasmic reticulum membrane Inferred from direct assay PubMed 10747087. Source: SGD mitochondrion Inferred from direct assay PubMed 14576278PubMed 16823961. 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_function	GTP 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...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
GDI1	P39958	8	EBI-29496,EBI-7517
YIF1	P53845	3	EBI-29496,EBI-28230
YIP3	P53633	2	EBI-29496,EBI-25301
YIP4	P53093	2	EBI-29496,EBI-24124

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

8

GTP By similarity

Nucleotide binding

63 – 67

5

GTP By similarity

Nucleotide binding

121 – 124

4

GTP By similarity

Region

63 – 80

18

Interaction with GDI1

Region

189 – 195

7

Interaction with GDI1

Motif

37 – 45

9

Effector region Probable

Amino acid modifications

Modified residue

1

1

N-acetylmethionine Ref.5

Modified residue

17

1

Phosphoserine Ref.24

Modified residue

172

1

Phosphoserine Ref.24

Modified residue

174

1

Phosphoserine Ref.23 Ref.24

Lipidation

205

1

S-geranylgeranyl cysteine Ref.14

Lipidation

206

1

S-geranylgeranyl cysteine Ref.14

Experimental info

Mutagenesis

17

1

S → G: Decreases GTP binding and increases GTP hydrolysis. Ref.6

Mutagenesis

21

1

K → M: Abolishes GTP binding. Ref.6

Mutagenesis

37

1

Y → F: No change. Ref.9

Mutagenesis

39

1

S → A: No change. Ref.9

Mutagenesis

40

1

T → S: No change. Ref.9

Mutagenesis

41

1

I → M: Lethal. Ref.9

Mutagenesis

43

1

V → E: No change. Ref.9

Mutagenesis

44

1

D → N: Temperature-sensitive phenotype. Ref.9

Mutagenesis

65

1

A → T: Decreases GTP binding and GTP hydrolysis. Ref.6

Mutagenesis

67

1

Q → L: Locks YPT1 in the GTP-bound form by reducing GTP hydrolysis rate 40-fold. Ref.12 Ref.22

Mutagenesis

121

1

N → I: Abolishes GTP binding. Ref.6

Mutagenesis

136

1

A → D: Loss of function at 37 degrees Celsius. Ref.9 Ref.10

Mutagenesis

205

1

C → S: Abolishes membrane association. Lethal; when associated with S-206. Ref.7 Ref.14

Mutagenesis

206

1

C → S: Abolishes membrane association. Lethal; when associated with S-205. Ref.7 Ref.14

Sequence conflict

171

1

E → Q in CAA25036. Ref.1

Secondary structure

1

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206

Helix Strand Turn

Details...

Beta strand

6 – 16

11

Helix

21 – 30

10

Beta strand

45 – 52

8

Beta strand

55 – 62

8

Turn

65 – 71

7

Helix

75 – 78

4

Beta strand

82 – 89

8

Helix

93 – 109

17

Beta strand

115 – 121

7

Turn

126 – 128

3

Helix

133 – 142

10

Beta strand

147 – 149

3

Turn

152 – 154

3

Helix

158 – 172

15

Helix

175 – 179

5

Helix

183 – 185

3

Sequences

	Sequence		Length	Mass (Da)
	P01123 [UniParc]. Last modified November 1, 1995. Version 2. Checksum: F8C704F6BF2D227B	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

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] [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 204511 / S288c / AB972.
[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. , 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, 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]	"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] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-174, MASS SPECTROMETRY.
[24]	"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-17; SER-172 AND SER-174, MASS SPECTROMETRY.
[25]	"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.

PIR

TVBYQ2. S56216.

RefSeq

NP_116615.1. NM_001179928.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1UKV	X-ray	1.50	Y	1-206	[»]
1YZN	X-ray	2.06	A	3-172	[»]
2BCG	X-ray	1.48	Y	1-206	[»]
3CUE	X-ray	3.70	F/L/R/X	1-206	[»]

ProteinModelPortal

P01123.

SMR

P01123. Positions 3-196.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-2019N.

IntAct

P01123. 23 interactions.

MINT

MINT-389361.

STRING

4932.YFL038C.

Proteomic databases

PaxDb

P01123.

PeptideAtlas

P01123.

PRIDE

P01123.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblFungi

YFL038C; YFL038C; YFL038C.

GeneID

850505.

KEGG

sce:YFL038C.

Organism-specific databases

CYGD

YFL038c.

SGD

S000001856. YPT1.

Phylogenomic databases

eggNOG

COG1100.

GeneTree

ENSGT00700000104049.

HOGENOM

HOG000233968.

KO

K07874.

OMA

MIMASEI.

OrthoDB

EOG49W5QK.

Gene expression databases

Genevestigator

P01123.

GermOnline

YFL038C. Saccharomyces cerevisiae.

Family and domain databases

InterPro

IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
IPR003579. Small_GTPase_Rab_type.
[Graphical view]

Pfam

PF00071. Ras. 1 hit.
[Graphical view]

PRINTS

PR00449. RASTRNSFRMNG.

SMART

SM00175. RAB. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00231. small_GTP. 1 hit.

PROSITE

PS51419. RAB. 1 hit.
[Graphical view]

ProtoNet

Search...

Other

EvolutionaryTrace

P01123.

NextBio

966209.

Entry information

Entry name

YPT1_YEAST

Accession

Primary (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 3, 2013
This is version 152 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Fungal Protein Annotation Program