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Protein

GTP-binding protein YPT1

Gene

YPT1

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to recruit to membranes different set of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion. YPT1 regulates the trafficking of secretory vesicles from the endoplasmic reticulum (ER) to the Golgi. 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. Plays a role in the initial events of the autophagic vacuole development which take place at specialized regions of the endoplasmic reticulum. Also involved in the recycling of membrane proteins.6 Publications

Enzyme regulationi

Rab activation is generally mediated by a guanine exchange factor (GEF), while inactivation through hydrolysis of bound GTP is catalyzed by a GTPase activating protein (GAP). YPT1 is activated by the GEFs DSS4 and TRAPP complex, and inactivated by GAPs GYP1, GYP5 and GYP8.4 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi15 – 23GTPBy similarity9
Nucleotide bindingi33 – 40GTPBy similarity8
Nucleotide bindingi63 – 67GTPBy similarity5
Nucleotide bindingi121 – 124GTPBy similarity4
Nucleotide bindingi151 – 153GTPBy similarity3

GO - Molecular functioni

  • GTPase activity Source: SGD
  • GTP binding Source: UniProtKB-KW
  • SNARE binding Source: SGD

GO - Biological processi

  • COPII-coated vesicle budding Source: SGD
  • CVT pathway Source: SGD
  • early endosome to Golgi transport Source: SGD
  • endocytic recycling Source: SGD
  • ER to Golgi vesicle-mediated transport Source: SGD
  • Golgi vesicle budding Source: SGD
  • Golgi vesicle docking Source: SGD
  • macroautophagy Source: SGD
  • pre-mRNA catabolic process Source: SGD
  • regulation of endoplasmic reticulum unfolded protein response Source: SGD
  • reticulophagy Source: SGD
  • retrograde vesicle-mediated transport, Golgi to ER Source: SGD
  • SNARE complex assembly Source: SGD
  • SNARE complex disassembly Source: SGD

Keywordsi

Biological processAutophagy, ER-Golgi transport, Protein transport, Transport
LigandGTP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-30424-MONOMER.
ReactomeiR-SCE-162658. Golgi Cisternae Pericentriolar Stack Reorganization.
R-SCE-204005. COPII (Coat Protein 2) Mediated Vesicle Transport.
R-SCE-6798695. Neutrophil degranulation.
R-SCE-6807878. COPI-mediated anterograde transport.
R-SCE-6811434. COPI-dependent Golgi-to-ER retrograde traffic.
R-SCE-6811440. Retrograde transport at the Trans-Golgi-Network.
R-SCE-8854214. TBC/RABGAPs.
R-SCE-8873719. RAB geranylgeranylation.

Names & Taxonomyi

Protein namesi
Recommended name:
GTP-binding protein YPT1
Alternative name(s):
Protein YP2
Rab GTPase YPT1
Transport GTPase YPT1
Gene namesi
Name:YPT1
Synonyms:YP2
Ordered Locus Names:YFL038C
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome VI

Organism-specific databases

EuPathDBiFungiDB:YFL038C.
SGDiS000001856. YPT1.

Subcellular locationi

GO - Cellular componenti

  • cis-Golgi network Source: SGD
  • cytoplasmic vesicle Source: SGD
  • cytosol Source: GOC
  • endoplasmic reticulum membrane Source: SGD
  • Golgi membrane Source: SGD
  • Golgi stack Source: SGD
  • pre-autophagosomal structure Source: SGD
  • pre-autophagosomal structure membrane Source: UniProtKB-SubCell

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Golgi apparatus, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi17S → G: Decreases GTP binding and increases GTP hydrolysis. 1 Publication1
Mutagenesisi21K → M: Abolishes GTP binding. 1 Publication1
Mutagenesisi37Y → F: No change. 1 Publication1
Mutagenesisi39S → A: No change. 1 Publication1
Mutagenesisi40T → S: No change. 1 Publication1
Mutagenesisi41I → M: Lethal. 1 Publication1
Mutagenesisi43V → E: No change. 1 Publication1
Mutagenesisi44D → N: Temperature-sensitive phenotype. 1 Publication1
Mutagenesisi65A → T: Decreases GTP binding and GTP hydrolysis. 1 Publication1
Mutagenesisi67Q → L: Locks YPT1 in the GTP-bound form by reducing GTP hydrolysis rate 40-fold. 2 Publications1
Mutagenesisi121N → I: Abolishes GTP binding. 1 Publication1
Mutagenesisi136A → D: Loss of function at 37 degrees Celsius. 1 Publication1
Mutagenesisi205C → S: Abolishes membrane association. Lethal; when associated with S-206. 2 Publications1
Mutagenesisi206C → S: Abolishes membrane association. Lethal; when associated with S-205. 2 Publications1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001213181 – 206GTP-binding protein YPT1Add BLAST206

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionine1 Publication1
Lipidationi23S-palmitoyl cysteineSequence analysis1
Lipidationi123S-palmitoyl cysteineSequence analysis1
Cross-linki144Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources
Modified residuei172PhosphoserineCombined sources1
Modified residuei174PhosphoserineCombined sources1
Lipidationi205S-geranylgeranyl cysteine1 Publication1
Lipidationi206S-geranylgeranyl cysteine1 Publication1

Post-translational modificationi

Prenylation is required for interaction with GDI1 and YIP1.1 Publication

Keywords - PTMi

Acetylation, Isopeptide bond, Lipoprotein, Palmitate, Phosphoprotein, Prenylation, Ubl conjugation

Proteomic databases

MaxQBiP01123.
PRIDEiP01123.

PTM databases

iPTMnetiP01123.

Interactioni

Subunit structurei

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 YIP5.5 Publications

Binary interactionsi

Show more details

GO - Molecular functioni

  • SNARE binding Source: SGD

Protein-protein interaction databases

BioGridi31108. 401 interactors.
DIPiDIP-2019N.
IntActiP01123. 23 interactors.
MINTiMINT-389361.
STRINGi4932.YFL038C.

Structurei

Secondary structure

1206
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 16Combined sources11
Helixi21 – 30Combined sources10
Beta strandi45 – 52Combined sources8
Beta strandi55 – 62Combined sources8
Turni65 – 71Combined sources7
Helixi75 – 78Combined sources4
Beta strandi82 – 89Combined sources8
Helixi93 – 109Combined sources17
Beta strandi115 – 121Combined sources7
Turni126 – 128Combined sources3
Helixi133 – 142Combined sources10
Beta strandi147 – 149Combined sources3
Turni152 – 154Combined sources3
Helixi158 – 172Combined sources15
Helixi175 – 179Combined sources5
Helixi183 – 185Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1UKVX-ray1.50Y1-206[»]
1YZNX-ray2.06A3-172[»]
2BCGX-ray1.48Y1-206[»]
3CUEX-ray3.70F/L/R/X1-206[»]
ProteinModelPortaliP01123.
SMRiP01123.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP01123.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni63 – 80Interaction with GDI1Add BLAST18
Regioni189 – 195Interaction with GDI17

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi37 – 45Effector regionCurated9

Sequence similaritiesi

Belongs to the small GTPase superfamily. Rab family.Curated

Phylogenomic databases

GeneTreeiENSGT00880000137860.
HOGENOMiHOG000233968.
InParanoidiP01123.
KOiK07874.
OMAiVTDNDTF.
OrthoDBiEOG092C5MDH.

Family and domain databases

InterProiView protein in InterPro
IPR027417. P-loop_NTPase.
IPR005225. Small_GTP-bd_dom.
IPR001806. Small_GTPase.
PfamiView protein in Pfam
PF00071. Ras. 1 hit.
SUPFAMiSSF52540. SSF52540. 1 hit.
TIGRFAMsiTIGR00231. small_GTP. 1 hit.
PROSITEiView protein in PROSITE
PS51419. RAB. 1 hit.

Sequencei

Sequence statusi: Complete.

P01123-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNSEYDYLFK LLLIGNSGVG KSCLLLRFSD DTYTNDYIST IGVDFKIKTV
60 70 80 90 100
ELDGKTVKLQ IWDTAGQERF RTITSSYYRG SHGIIIVYDV TDQESFNGVK
110 120 130 140 150
MWLQEIDRYA TSTVLKLLVG NKCDLKDKRV VEYDVAKEFA DANKMPFLET
160 170 180 190 200
SALDSTNVED AFLTMARQIK ESMSQQNLNE TTQKKEDKGN VNLKGQSLTN

TGGGCC
Length:206
Mass (Da):23,214
Last modified:November 1, 1995 - v2
Checksum:iF8C704F6BF2D227B
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti171E → Q in CAA25036 (PubMed:6318115).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X00209 Genomic DNA. Translation: CAA25036.1.
D50617 Genomic DNA. Translation: BAA09201.1.
AY558467 Genomic DNA. Translation: AAS56793.1.
BK006940 Genomic DNA. Translation: DAA12402.1.
PIRiS56216. TVBYQ2.
RefSeqiNP_116615.1. NM_001179928.1.

Genome annotation databases

EnsemblFungiiBAA09201; BAA09201; BAA09201.
YFL038C; YFL038C; YFL038C.
GeneIDi850505.
KEGGisce:YFL038C.

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

Entry informationi

Entry nameiYPT1_YEAST
AccessioniPrimary (citable) accession number: P01123
Secondary accession number(s): D6VTJ2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: November 1, 1995
Last modified: July 5, 2017
This is version 193 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Caution

In PubMed:3042385 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.Curated

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, 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 VI
    Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names