3W1S

Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the N-terminal domain of Atg16


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating Atg8-PE conjugation

Noda, N.N.Fujioka, Y.Hanada, T.Ohsumi, Y.Inagaki, F.

(2013) EMBO Rep 14: 206-211

  • DOI: 10.1038/embor.2012.208
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Atg12 is conjugated to Atg5 through enzymatic reactions similar to ubiquitination. The Atg12-Atg5 conjugate functions as an E3-like enzyme to promote lipidation of Atg8, whereas lipidated Atg8 has essential roles in both autophagosome formation and s ...

    Atg12 is conjugated to Atg5 through enzymatic reactions similar to ubiquitination. The Atg12-Atg5 conjugate functions as an E3-like enzyme to promote lipidation of Atg8, whereas lipidated Atg8 has essential roles in both autophagosome formation and selective cargo recognition during autophagy. However, the molecular role of Atg12 modification in these processes has remained elusive. Here, we report the crystal structure of the Atg12-Atg5 conjugate. In addition to the isopeptide linkage, Atg12 forms hydrophobic and hydrophilic interactions with Atg5, thereby fixing its position on Atg5. Structural comparison with unmodified Atg5 and mutational analyses showed that Atg12 modification neither induces a conformational change in Atg5 nor creates a functionally important architecture. Rather, Atg12 functions as a binding module for Atg3, the E2 enzyme for Atg8, thus endowing Atg5 with the ability to interact with Atg3 to facilitate Atg8 lipidation.


    Organizational Affiliation

    Microbial Chemistry Research Foundation, Laboratory of Molecular Structure, Institute of Microbial Chemistry, 3-14-23, Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan. nn@bikaken.or.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Autophagy protein 16
B
49Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: APG15APG16ATG16Atg16(amino acids 1-46)CVT11SAP18YM8520.08CYMR159C
Find proteins for Q03818 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03818

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-like protein ATG12
C
91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: APG12ATG12Atg12(amino acids 100-186)YBR1506YBR217W
Find proteins for P38316 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38316

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Autophagy protein 5
A
284Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: APG5ATG5Atg5(amino acids 1-284)P2601YPL149W
Find proteins for Q12380 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12380
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.231 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.149α = 90
b = 106.084β = 90
c = 143.071γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-06-26
    Changes: Database references