3VX6

Crystal structure of Kluyveromyces marxianus Atg7NTD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.

Yamaguchi, M.Matoba, K.Sawada, R.Fujioka, Y.Nakatogawa, H.Yamamoto, H.Kobashigawa, Y.Hoshida, H.Akada, R.Ohsumi, Y.Noda, N.N.Inagaki, F.

(2012) Nat Struct Mol Biol 19: 1250-1256

  • DOI: https://doi.org/10.1038/nsmb.2451
  • Primary Citation of Related Structures:  
    3VX6, 3VX7, 3VX8

  • PubMed Abstract: 

    Autophagy requires ubiquitin-like Atg8 and Atg12 conjugation systems, where Atg7 has a critical role as the sole E1 enzyme. Although Atg7 recognizes two distinct E2s, Atg3 and Atg10, it is not understood how Atg7 correctly loads these E2s with their cognate ubiquitin-like proteins, Atg8 and Atg12. Here, we report the crystal structures of the N-terminal domain of Atg7 bound to Atg10 or Atg3 of thermotolerant yeast and plant homologs. The observed Atg7-Atg10 and Atg7-Atg3 interactions, which resemble each other but are quite distinct from the canonical E1-E2 interaction, makes Atg7 suitable for transferring Atg12 to Atg10 and Atg8 to Atg3 by a trans mechanism. Notably, in vitro experiments showed that Atg7 loads Atg3 and Atg10 with Atg8 and Atg12 in a nonspecific manner, which suggests that cognate conjugate formation in vivo is not an intrinsic quality of Atg7.


  • Organizational Affiliation

    Department of Structural Biology, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E1283Kluyveromyces marxianusMutation(s): 0 
UniProt
Find proteins for L7MTK3 (Kluyveromyces marxianus)
Explore L7MTK3 
Go to UniProtKB:  L7MTK3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL7MTK3
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.224 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.908α = 90
b = 118.908β = 90
c = 45.05γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-08
    Changes: Refinement description