UniProtKB - P01123 (YPT1_YEAST)
GTP-binding protein YPT1
YPT1
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 PublicationsCaution
Activity regulationi
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Binding sitei | 66 | GTP; via amide nitrogenCombined sources1 Publication | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 17 – 23 | GTPCombined sources3 Publications | 7 | |
Nucleotide bindingi | 33 – 40 | GTPCombined sources3 Publications | 8 | |
Nucleotide bindingi | 121 – 124 | GTPCombined sources3 Publications | 4 | |
Nucleotide bindingi | 152 – 153 | GTPCombined sources3 Publications | 2 |
GO - Molecular functioni
- GTPase activity Source: SGD
- GTP binding Source: UniProtKB-KW
- SNARE binding Source: SGD
GO - Biological processi
- autophagosome assembly Source: GO_Central
- COPII-coated vesicle budding Source: SGD
- cytoplasm to vacuole transport by the Cvt pathway Source: SGD
- early endosome to Golgi transport Source: SGD
- endocytic recycling Source: SGD
- endoplasmic reticulum to Golgi vesicle-mediated transport Source: SGD
- Golgi vesicle budding Source: SGD
- Golgi vesicle docking Source: SGD
- intracellular protein transport Source: GO_Central
- macroautophagy Source: SGD
- pre-mRNA catabolic process Source: SGD
- protein localization to phagophore assembly site Source: SGD
- regulation of endoplasmic reticulum unfolded protein response Source: SGD
- regulation of kinase activity Source: SGD
- reticulophagy Source: SGD
- retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum Source: SGD
- SNARE complex assembly Source: SGD
- SNARE complex disassembly Source: SGD
Keywordsi
Biological process | Autophagy, ER-Golgi transport, Protein transport, Transport |
Ligand | GTP-binding, Nucleotide-binding |
Enzyme and pathway databases
Reactomei | R-SCE-162658, Golgi Cisternae Pericentriolar Stack Reorganization R-SCE-204005, COPII-mediated vesicle transport R-SCE-6807878, COPI-mediated anterograde transport R-SCE-6811434, COPI-dependent Golgi-to-ER retrograde traffic R-SCE-8873719, RAB geranylgeranylation R-SCE-8876198, RAB GEFs exchange GTP for GDP on RABs |
Names & Taxonomyi
Protein namesi | Recommended name: GTP-binding protein YPT1Alternative name(s): Protein YP2 Rab GTPase YPT1 Transport GTPase YPT1 |
Gene namesi | Name:YPT1 Synonyms:YP2 Ordered Locus Names:YFL038C |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000001856, YPT1 |
VEuPathDBi | FungiDB:YFL038C |
Subcellular locationi
Endoplasmic reticulum
- Endoplasmic reticulum membrane 1 Publication; Peripheral membrane protein 1 Publication
Cytoplasm and Cytosol
- Cytoplasm 1 Publication
Golgi apparatus
- Golgi apparatus membrane 1 Publication; Peripheral membrane protein 1 Publication
Other locations
- Preautophagosomal structure membrane 1 Publication; Lipid-anchor Curated; Cytoplasmic side Curated
Note: ER and Golgi when GTP-bound. Cytoplasmic when bound to GDI1.
Cytosol
- cytosol Source: GOC
Endoplasmic reticulum
- endoplasmic reticulum membrane Source: SGD
Golgi apparatus
- cis-Golgi network Source: SGD
- Golgi membrane Source: SGD
- Golgi stack Source: SGD
Mitochondrion
- mitochondrion Source: SGD
Other locations
- cytoplasmic vesicle Source: SGD
- endomembrane system Source: GO_Central
- phagophore assembly site Source: SGD
- phagophore assembly site membrane Source: UniProtKB-SubCell
Keywords - Cellular componenti
Cytoplasm, Endoplasmic reticulum, Golgi apparatus, MembranePathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 17 | S → G: Decreases GTP binding and increases GTP hydrolysis. 1 Publication | 1 | |
Mutagenesisi | 21 | K → M: Abolishes GTP binding. 1 Publication | 1 | |
Mutagenesisi | 37 | Y → F: No change. 1 Publication | 1 | |
Mutagenesisi | 39 | S → A: No change. 1 Publication | 1 | |
Mutagenesisi | 40 | T → S: No change. 1 Publication | 1 | |
Mutagenesisi | 41 | I → M: Lethal. 1 Publication | 1 | |
Mutagenesisi | 43 | V → E: No change. 1 Publication | 1 | |
Mutagenesisi | 44 | D → N: Temperature-sensitive phenotype. 1 Publication | 1 | |
Mutagenesisi | 65 | A → T: Decreases GTP binding and GTP hydrolysis. 1 Publication | 1 | |
Mutagenesisi | 67 | Q → L: Locks YPT1 in the GTP-bound form by reducing GTP hydrolysis rate 40-fold. 2 Publications | 1 | |
Mutagenesisi | 121 | N → I: Abolishes GTP binding. 1 Publication | 1 | |
Mutagenesisi | 136 | A → D: Loss of function at 37 degrees Celsius. 1 Publication | 1 | |
Mutagenesisi | 205 | C → S: Abolishes membrane association. Lethal; when associated with S-206. 2 Publications | 1 | |
Mutagenesisi | 206 | C → S: Abolishes membrane association. Lethal; when associated with S-205. 2 Publications | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000121318 | 1 – 206 | GTP-binding protein YPT1Add BLAST | 206 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 1 | N-acetylmethionine1 Publication | 1 | |
Lipidationi | 23 | S-palmitoyl cysteineSequence analysis | 1 | |
Lipidationi | 123 | S-palmitoyl cysteineSequence analysis | 1 | |
Cross-linki | 144 | Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)Combined sources | ||
Modified residuei | 172 | PhosphoserineCombined sources | 1 | |
Modified residuei | 174 | PhosphoserineCombined sources | 1 | |
Lipidationi | 205 | S-geranylgeranyl cysteine2 Publications | 1 | |
Lipidationi | 206 | S-geranylgeranyl cysteineCombined sources3 Publications | 1 |
Post-translational modificationi
Keywords - PTMi
Acetylation, Isopeptide bond, Lipoprotein, Palmitate, Phosphoprotein, Prenylation, Ubl conjugationProteomic databases
MaxQBi | P01123 |
PaxDbi | P01123 |
PRIDEi | P01123 |
PTM databases
iPTMneti | P01123 |
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 PublicationsBinary interactionsi
P01123
GO - Molecular functioni
- SNARE binding Source: SGD
Protein-protein interaction databases
BioGRIDi | 31108, 433 interactors |
DIPi | DIP-2019N |
IntActi | P01123, 34 interactors |
MINTi | P01123 |
STRINGi | 4932.YFL038C |
Miscellaneous databases
RNActi | P01123, protein |
Structurei
Secondary structure
3D structure databases
SMRi | P01123 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P01123 |
Family & Domainsi
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 63 – 80 | Interaction with GDI11 PublicationAdd BLAST | 18 | |
Regioni | 173 – 206 | DisorderedSequence analysisAdd BLAST | 34 | |
Regioni | 189 – 195 | Interaction with GDI11 Publication | 7 |
Motif
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Motifi | 37 – 45 | Effector regionCurated | 9 |
Compositional bias
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Compositional biasi | 192 – 206 | Polar residuesSequence analysisAdd BLAST | 15 |
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG0084, Eukaryota |
GeneTreei | ENSGT00940000175199 |
HOGENOMi | CLU_041217_23_1_1 |
InParanoidi | P01123 |
OMAi | KERMGNT |
Family and domain databases
Gene3Di | 3.40.50.300, 1 hit |
InterProi | View protein in InterPro IPR027417, P-loop_NTPase IPR005225, Small_GTP-bd_dom IPR001806, Small_GTPase |
Pfami | View protein in Pfam PF00071, Ras, 1 hit |
SMARTi | View protein in SMART SM00174, RHO, 1 hit |
SUPFAMi | SSF52540, SSF52540, 1 hit |
TIGRFAMsi | TIGR00231, small_GTP, 1 hit |
PROSITEi | View protein in PROSITE PS51419, RAB, 1 hit |
i Sequence
Sequence statusi: Complete.
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
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 |
PIRi | S56216, TVBYQ2 |
RefSeqi | NP_116615.1, NM_001179928.1 |
Genome annotation databases
EnsemblFungii | YFL038C_mRNA; YFL038C; YFL038C |
GeneIDi | 850505 |
KEGGi | sce:YFL038C |
Similar proteinsi
Cross-referencesi
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 |
PIRi | S56216, TVBYQ2 |
RefSeqi | NP_116615.1, NM_001179928.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB 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 | [»] | |
7KMT | electron microscopy | 3.70 | A | 1-206 | [»] | |
SMRi | P01123 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 31108, 433 interactors |
DIPi | DIP-2019N |
IntActi | P01123, 34 interactors |
MINTi | P01123 |
STRINGi | 4932.YFL038C |
PTM databases
iPTMneti | P01123 |
Proteomic databases
MaxQBi | P01123 |
PaxDbi | P01123 |
PRIDEi | P01123 |
Genome annotation databases
EnsemblFungii | YFL038C_mRNA; YFL038C; YFL038C |
GeneIDi | 850505 |
KEGGi | sce:YFL038C |
Organism-specific databases
SGDi | S000001856, YPT1 |
VEuPathDBi | FungiDB:YFL038C |
Phylogenomic databases
eggNOGi | KOG0084, Eukaryota |
GeneTreei | ENSGT00940000175199 |
HOGENOMi | CLU_041217_23_1_1 |
InParanoidi | P01123 |
OMAi | KERMGNT |
Enzyme and pathway databases
Reactomei | R-SCE-162658, Golgi Cisternae Pericentriolar Stack Reorganization R-SCE-204005, COPII-mediated vesicle transport R-SCE-6807878, COPI-mediated anterograde transport R-SCE-6811434, COPI-dependent Golgi-to-ER retrograde traffic R-SCE-8873719, RAB geranylgeranylation R-SCE-8876198, RAB GEFs exchange GTP for GDP on RABs |
Miscellaneous databases
EvolutionaryTracei | P01123 |
PROi | PR:P01123 |
RNActi | P01123, protein |
Family and domain databases
Gene3Di | 3.40.50.300, 1 hit |
InterProi | View protein in InterPro IPR027417, P-loop_NTPase IPR005225, Small_GTP-bd_dom IPR001806, Small_GTPase |
Pfami | View protein in Pfam PF00071, Ras, 1 hit |
SMARTi | View protein in SMART SM00174, RHO, 1 hit |
SUPFAMi | SSF52540, SSF52540, 1 hit |
TIGRFAMsi | TIGR00231, small_GTP, 1 hit |
PROSITEi | View protein in PROSITE PS51419, RAB, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | YPT1_YEAST | |
Accessioni | P01123Primary (citable) accession number: P01123 Secondary accession number(s): D6VTJ2 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | July 21, 1986 |
Last sequence update: | November 1, 1995 | |
Last modified: | February 23, 2022 | |
This is version 223 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome VI
Yeast (Saccharomyces cerevisiae) chromosome VI: entries and gene names - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families