PDBsum entry 6rgo

Lipid binding protein

PDB id: 6rgo

Contents

Protein chains

327 a.a.

38 a.a.

35 a.a.

PDB id:

6rgo

Name:

Lipid binding protein

Title:

Complex of klatg21 with coiled-coil of agatg16

Structure:

Autophagy-related protein 21. Chain: a, b. Engineered: yes. Autophagy protein 16. Chain: c, d. Engineered: yes

Source:

Kluyveromyces lactis (strain atcc 8585 / cbs 2359 / dsm 70799 / nbrc 1267 / nrrl y-1140 / wm37). Yeast. Organism_taxid: 284590. Strain: atcc 8585 / cbs 2359 / dsm 70799 / nbrc 1267 / nrrl y-1140 / wm37. Gene: atg21, klla0e24354g. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.70Å R-factor: 0.286 R-free: 0.307

Authors:

M.Thumm,P.Neumann

Key ref:

L.Munzel et al. (2021). Atg21 organizes Atg8 lipidation at the contact of the vacuole with the phagophore. Autophagy, 17, 1458-1478. PubMed id: 32515645 DOI: 10.1080/15548627.2020.1766332

Date:

17-Apr-19 Release date: 13-May-20

Protein chains

Q6CLZ2  (ATG21_KLULA) -  Autophagy-related protein 21 from Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)

Seq: 392 a.a.

Struc: 327 a.a.

Protein chain

Q755K3  (ATG16_ASHGO) -  Autophagy protein 16 from Eremothecium gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)

Seq: 124 a.a.

Struc: 38 a.a.

Protein chain

Q755K3  (ATG16_ASHGO) -  Autophagy protein 16 from Eremothecium gossypii (strain ATCC 10895 / CBS 109.51 / FGSC 9923 / NRRL Y-1056)

Seq: 124 a.a.

Struc: 35 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.?

DOI no: 10.1080/15548627.2020.1766332

Autophagy 17:1458-1478 (2021)

PubMed id: 32515645

Atg21 organizes Atg8 lipidation at the contact of the vacuole with the phagophore.

L.Munzel, P.Neumann, F.B.Otto, R.Krick, J.Metje-Sprink, B.Kroppen, N.Karedla, J.Enderlein, M.Meinecke, R.Ficner, M.Thumm.

ABSTRACT

Coupling of Atg8 to phosphatidylethanolamine is crucial for the expansion of the crescent-shaped phagophore during cargo engulfment. Atg21, a PtdIns3P-binding beta-propeller protein, scaffolds Atg8 and its E3-like complex Atg12-Atg5-Atg16 during lipidation. The crystal structure of Atg21, in complex with the Atg16 coiled-coil domain, showed its binding at the bottom side of the Atg21 beta-propeller. Our structure allowed detailed analyses of the complex formation of Atg21 with Atg16 and uncovered the orientation of the Atg16 coiled-coil domain with respect to the membrane. We further found that Atg21 was restricted to the phagophore edge, near the vacuole, known as the vacuole isolation membrane contact site (VICS). We identified a specialized vacuolar subdomain at the VICS, typical of organellar contact sites, where the membrane protein Vph1 was excluded, while Vac8 was concentrated. Furthermore, Vac8 was required for VICS formation. Our results support a specialized organellar contact involved in controlling phagophore elongation. Abbreviations: FCCS: fluorescence cross correlation spectroscopy; NVJ: nucleus-vacuole junction; PAS: phagophore assembly site; PE: phosphatidylethanolamine; PROPPIN: beta-propeller that binds phosphoinositides; PtdIns3P: phosphatidylinositol- 3-phosphate; VICS: vacuole isolation membrane contact site.