7EU4 image
Entry Detail
PDB ID:
7EU4
Keywords:
Title:
Crystal structure of plant ATG12 complexed with the AIM12 of ATG3
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2021-05-16
Release Date:
2021-07-28
Method Details:
Experimental Method:
Resolution:
3.20 Å
R-Value Free:
0.28
R-Value Work:
0.23
Space Group:
P 64
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Ubiquitin-like protein ATG12B
Chain IDs:A, B, C, D, E, F, G, H, I, J, K, L, M, N
Chain Length:96
Number of Molecules:14
Biological Source:Arabidopsis thaliana
Polymer Type:polypeptide(L)
Description:AIM12 from Autophagy-related protein 3
Chain IDs:O, P, Q, R
Chain Length:11
Number of Molecules:4
Biological Source:Arabidopsis thaliana
Ligand Molecules
Primary Citation
Atg12-Interacting Motif Is Crucial for E2-E3 Interaction in Plant Atg8 System.
Biol.Pharm.Bull. 44 1337 1343 (2021)
PMID: 34193767 DOI: 10.1248/bpb.b21-00439

Abstact

Autophagy is an intracellular degradation system regulating cellular homeostasis. The two ubiquitin-like modification systems named the Atg8 system and the Atg12 system are essential for autophagy. Atg8 and Atg12 are ubiquitin-like proteins covalently conjugated with a phosphatidylethanolamine (PE) and Atg5, respectively, via enzymatic reactions. The Atg8-PE conjugate binds to autophagic membranes and recruits various proteins through direct interaction, whereas the Atg12-Atg5 conjugate recognizes Atg3, the E2 enzyme for Atg8, and facilitates Atg8-PE conjugation by functioning as the E3 enzyme. Although structural and biochemical analyses have well established the Atg8-family interacting motif (AIM), studies on the interacting sequence for Atg12 are rare (only one example for human ATG12-ATG3), thereby making it challenging to define a binding motif. Here we determined the crystal structure of the plant ATG12b as a complex with the ATG12b-binding region of ATG3 and revealed that ATG12b recognizes the aspartic acid (Asp)-methionine (Met) motif in ATG3 via a hydrophobic pocket and a basic residue, which we confirmed critical for the complex formation by mutational analysis. This recognition mode is similar to that reported between human ATG12 and ATG3, suggesting that the Asp-Met sequence is a conserved Atg12-interacting motif (AIM12). These data suggest that AIM12 mediates E2-E3 interaction during Atg8 lipidation and provide structural basis for developing chemicals that regulate autophagy by targeting Atg12-family proteins.

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Primary Citation of related structures