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TitleStructure of yeast Ape1 and its role in autophagic vesicle formation.
Journal, issue, pagesAutophagy, Vol. 11, Issue 9, Page 1580-1593, Year 2015
Publish dateJun 20, 2016
AuthorsMing-Yuan Su / Wen-Hsin Peng / Meng-Ru Ho / Shih-Chieh Su / Yuan-Chih Chang / Guang-Chao Chen / Chung-I Chang /
PubMed AbstractIn Saccharomyces cerevisiae, a constitutive biosynthetic transport pathway, termed the cytoplasm-to-vacuole targeting (Cvt) pathway, sequesters precursor aminopeptidase I (prApe1) dodecamers in the ...In Saccharomyces cerevisiae, a constitutive biosynthetic transport pathway, termed the cytoplasm-to-vacuole targeting (Cvt) pathway, sequesters precursor aminopeptidase I (prApe1) dodecamers in the form of a large complex into a Cvt vesicle using autophagic machinery, targeting it into the vacuole (the yeast lysosome) where it is proteolytically processed into its mature form, Ape1, by removal of an amino-terminal 45-amino acid propeptide. prApe1 is thought to serve as a scaffolding cargo critical for the assembly of the Cvt vesicle by presenting the propeptide to mediate higher-ordered complex formation and autophagic receptor recognition. Here we report the X-ray crystal structure of Ape1 at 2.5 Å resolution and reveal its dodecameric architecture consisting of dimeric and trimeric units, which associate to form a large tetrahedron. The propeptide of prApe1 exhibits concentration-dependent oligomerization and forms a stable tetramer. Structure-based mutagenesis demonstrates that disruption of the inter-subunit interface prevents dodecameric assembly and vacuolar targeting in vivo despite the presence of the propeptide. Furthermore, by examining the vacuolar import of propeptide-fused exogenous protein assemblies with different quaternary structures, we found that 3-dimensional spatial distribution of propeptides presented by a scaffolding cargo is essential for the assembly of the Cvt vesicle for vacuolar delivery. This study describes a molecular framework for understanding the mechanism of Cvt or autophagosomal biogenesis in selective macroautophagy.
External linksAutophagy / PubMed:26208681 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.5 - 19.0 Å
Structure data

EMDB-6265:
Three-dimensional reconstruction of yeast Ape1
Method: EM (single particle) / Resolution: 19.0 Å

PDB-4r8f:
Crystal structure of yeast aminopeptidase 1 (Ape1)
Method: X-RAY DIFFRACTION / Resolution: 2.5 Å

Chemicals

ChemComp-HOH:
WATER / Water

Source
  • Saccharomyces cerevisiae (brewer's yeast)
  • saccharomyces cerevisiae s288c (yeast)
KeywordsHYDROLASE / peptidase / Cvt pathway / Autophagy

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