Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36263.29 
• Atom Count: 1676 
• Residue Count: 312 
• Unique protein chains: 1

2DYT

The crystal structure of Saccharomyces cerevisiae Atg3

• DOI: 10.2210/pdb2DYT/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
• Expression System: Escherichia coli


• Deposited: 2006-09-17 Released: 2007-01-23 
• Deposition Author(s): Yamada, Y., Suzuki, N.N., Inagaki, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 

Literature

The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation

Yamada, Y., Suzuki, N.N., Hanada, T., Ichimura, Y., Kumeta, H., Fujioka, Y., Ohsumi, Y., Inagaki, F.

(2007) J.Biol.Chem. 282: 8036-8043

• PubMed: 17227760 
• DOI: 10.1074/jbc.M611473200


• PubMed Abstract: 
  

Atg3 is an E2-like enzyme that catalyzes the conjugation of Atg8 and phosphatidylethanolamine (PE). The Atg8-PE conjugate is essential for autophagy, which is the bulk degradation process of cytoplasmic components by the vacuolar/lysosomal system. We report here the crystal structure of Saccharomyces cerevisiae Atg3 at 2.5-A resolution. Atg3 has an alpha/beta-fold, and its core region is topologically similar to canonical E2 enzymes. Atg3 has two regions inserted in the core region, one of which consists of approximately 80 residues and has a random coil structure in solution and another with a long alpha-helical structure that protrudes from the core region as far as 30 A. In vivo and in vitro analyses suggested that the former region is responsible for binding Atg7, an E1-like enzyme, and that the latter is responsible for binding Atg8. A sulfate ion was bound near the catalytic cysteine of Atg3, suggesting a possible binding site for the phosphate moiety of PE. The structure of Atg3 provides a molecular basis for understanding the unique lipidation reaction that Atg3 carries out.

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Related Citations: 

• Crystallization and preliminary X-ray analysis of Atg3
  Yamada, Y.,Suzuki, N.N.,Fujioka, Y.,Ichimura, Y.,Ohsumi, Y.,Inagaki, F.
  (2006) ACTA CRYSTALLOGR.,SECT.F 62: 1016




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Organizational Affiliation: 

Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Hokkaido University, N-12, W-6, Kita-ku, Sapporo 060-0812, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Autophagy-related protein 3	A	312	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	Mutation(s): 0  Gene Names: ATG3 (APG3, AUT1)
Find proteins for P40344 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Go to Gene View: ATG3 Go to UniProtKB:  P40344

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 
• Space Group: P 4₁

Unit Cell:

Length (Å)	Angle (°)
a = 59.116	α = 90.00
b = 59.116	β = 90.00
c = 115.316	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data collection
SOLVE	phasing
CNS	refinement
HKL-2000	data scaling
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-09-17 
• Released Date: 2007-01-23 
• Deposition Author(s): Yamada, Y., Suzuki, N.N., Inagaki, F.

Revision History 

• Version 1.0: 2007-01-23
  Type: Initial release
• Version 1.1: 2007-10-08
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance