5YEC

Crystal structure of Atg7CTD-Atg8-MgATP complex in form II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


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Literature

Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition.

Yamaguchi, M.Satoo, K.Suzuki, H.Fujioka, Y.Ohsumi, Y.Inagaki, F.Noda, N.N.

(2018) J Mol Biol 430: 249-257

  • DOI: 10.1016/j.jmb.2017.12.002
  • Primary Citation of Related Structures:  
    5YEC

  • PubMed Abstract: 
  • Atg8 is a unique ubiquitin-like protein that is covalently conjugated with a phosphatidylethanolamine through reactions similar to ubiquitination and plays essential roles in autophagy. Atg7 is the E1 enzyme for Atg8, and it activates the C-terminal Gly116 of Atg8 using ATP ...

    Atg8 is a unique ubiquitin-like protein that is covalently conjugated with a phosphatidylethanolamine through reactions similar to ubiquitination and plays essential roles in autophagy. Atg7 is the E1 enzyme for Atg8, and it activates the C-terminal Gly116 of Atg8 using ATP. Here, we report the crystal structure of Atg8 bound to the C-terminal domain of Atg7 in an unprecedented mode. Atg8 neither contacts with the central β-sheet nor binds to the catalytic site of Atg7, both of which were observed in previously reported Atg7-Atg8 structures. Instead, Atg8 binds to the C-terminal α-helix and crossover loop, thereby changing the autoinhibited conformation of the crossover loop observed in the free Atg7 structure into a short helix and a disordered loop. Mutational analyses suggested that this interaction mode is important for the activation reaction. We propose that Atg7 recognizes Atg8 through multiple steps, which would be necessary to induce a conformational change in Atg7 that is optimal for the activation reaction.


    Organizational Affiliation

    Institute of Microbial Chemistry (BIKAKEN), Tokyo 141-0021, Japan. Electronic address: nn@bikaken.or.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-like modifier-activating enzyme ATG7 AC340Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ATG7APG7CVT2YHR171W
Find proteins for P38862 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38862 
Go to UniProtKB:  P38862
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Autophagy-related protein 8 BD119Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: ATG8APG8AUT7CVT5YBL078CYBL0732
Find proteins for P38182 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38182 
Go to UniProtKB:  P38182
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.995α = 90
b = 138.995β = 90
c = 134.368γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release