We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

6kbn

From Proteopedia

Jump to: navigation, search

Crystal structure of Vac8 (del 19-33) bound to Atg13

Structural highlights

6kbn is a 4 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.2Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

VAC8_YEAST Functions in both vacuole inheritance and protein targeting from the cytoplasm to vacuole.^[1]

Publication Abstract from PubMed

Armadillo (ARM) repeat proteins constitute a large protein family with diverse and fundamental functions in all organisms, and armadillo repeat domains share high structural similarity. However, exactly how these structurally similar proteins can mediate diverse functions remains a long-standing question. Vac8 (vacuole related 8) is a multifunctional protein that plays pivotal roles in various autophagic pathways, including piecemeal microautophagy of the nucleus (PMN) and cytoplasm-to-vacuole targeting (Cvt) pathways in the budding yeast Saccharomyces cerevisiae. Vac8 comprises an H1 helix at the N terminus, followed by 12 armadillo repeats. Herein, we report the crystal structure of Vac8 bound to Atg13, a key component of autophagic machinery. The 70-A extended loop of Atg13 binds to the ARM domain of Vac8 in an antiparallel manner. Structural, biochemical, and in vivo experiments demonstrated that the H1 helix of Vac8 intramolecularly associates with the first ARM and regulates its self-association, which is crucial for Cvt and PMN pathways. The structure of H1 helix-deleted Vac8 complexed with Atg13 reveals that Vac8[Delta19-33]-Atg13 forms a heterotetramer and adopts an extended superhelical structure exclusively employed in the Cvt pathway. Most importantly, comparison of Vac8-Nvj1 and Vac8-Atg13 provides a molecular understanding of how a single ARM domain protein adopts different quaternary structures depending on its associated proteins to differentially regulate 2 closely related but distinct cellular pathways. Abbreviations : Ape1: aminopeptidase I; ARM: armadillo repeat; Atg: autophagy-related; AUC: analytical ultracentrifugation; Cvt: cytoplasm-to-vacuole targeting; DIC: differential interference contrast; GFP: green fluorescent protein; GST: glutathione-S-transferase; ITC: isothermal titration calorimetry; NVJ: nucleus-vacuole junction; PDB: protein data bank; PMN: piecemeal microautophagy of the nucleus; prApe1: precursor Ape1; RMSD: root-mean-square deviation; SAXS: small-angle X-ray scattering; SD-N: nitrogen starvation medium; SEC: size-exclusion chromatography; tAtg13: Atg13 construct comprising residues 567-695; tNvj1: Nvj1 construct comprising residues 229-321; tVac8: Vac8 construct comprising residues 10-515; Vac8: vacuole related 8.

Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways.,Park J, Kim HI, Jeong H, Lee M, Jang SH, Yoon SY, Kim H, Park ZY, Jun Y, Lee C Autophagy. 2019 Sep 12:1-16. doi: 10.1080/15548627.2019.1659615. PMID:31512555^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Wang YX, Catlett NL, Weisman LS. Vac8p, a vacuolar protein with armadillo repeats, functions in both vacuole inheritance and protein targeting from the cytoplasm to vacuole. J Cell Biol. 1998 Mar 9;140(5):1063-74. PMID:9490720
↑ Park J, Kim HI, Jeong H, Lee M, Jang SH, Yoon SY, Kim H, Park ZY, Jun Y, Lee C. Quaternary structures of Vac8 differentially regulate the Cvt and PMN pathways. Autophagy. 2019 Sep 12:1-16. doi: 10.1080/15548627.2019.1659615. PMID:31512555 doi:http://dx.doi.org/10.1080/15548627.2019.1659615