PDBsum entry 2dyt

Ligase

PDB id: 2dyt

Contents

Protein chain

213 a.a. *

Ligands

SO4 ×2

Waters ×46

* Residue conservation analysis

PDB id:

2dyt

Name:

Ligase

Title:

The crystal structure of saccharomyces cerevisiae atg3

Structure:

Autophagy-related protein 3. Chain: a. Synonym: autophagy-related e2-like conjugation enzyme atg3. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.50Å R-factor: 0.207 R-free: 0.244

Authors:

Y.Yamada,N.N.Suzuki,F.Inagaki

Key ref:

Y.Yamada et al. (2007). The crystal structure of Atg3, an autophagy-related ubiquitin carrier protein (E2) enzyme that mediates Atg8 lipidation. J Biol Chem, 282, 8036-8043. PubMed id: 17227760 DOI: 10.1074/jbc.M611473200

Date:

17-Sep-06 Release date: 23-Jan-07

Protein chain

P40344  (ATG3_YEAST) -  Autophagy-related protein 3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 310 a.a.

Struc: 213 a.a.

DOI no: 10.1074/jbc.M611473200

J Biol Chem 282:8036-8043 (2007)

PubMed id: 17227760

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

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

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.

Selected figure(s)

Figure 1.
FIGURE 1. A, stereo view of the ribbon diagram of Atg3. The -helices are lettered and indicated with red helical ribbons, and -strands are numbered and indicated with cyan arrows. Residues adjacent to the disordered regions are numbered. B, structural comparison of Atg3 with Ubc9. Ribbon diagrams (top) and topologies (bottom) of Atg3 and Ubc9 (Protein Data Bank code 1U9A) are shown in the same orientation. Conserved -helices and -strands are colored red and cyan, respectively, and nonconserved -helices, -strands, and loop regions are colored gray. The two unique inserted regions of Atg3, FR and HR, are colored yellow. Numbering and labeling of secondary structural elements are based on Atg3. Amino and carboxyl termini are denoted N and C, respectively, and the catalytic cysteine of Atg3 and Ubc9 is indicated with a stick model (top) and a circled letter (bottom). C, ribbon diagram of the catalytic site of Atg3 (left) and Ubc9 (right). The side chains of Cys-234 (Atg3) and Cys-93 (Ubc9) as well as their surrounding residues are shown with stick models and are colored yellow, red, and blue for sulfur, oxygen, and nitrogen atoms, respectively. A sulfate ion observed in the Atg3 structure is also shown with a stick model. Hydrogen bonds between Pro-233 and Val-239 of Atg3 and between Cys-93 and Asn-85 of Ubc9 are shown with broken lines. The figure was prepared using PyMOL (35).

Figure 6.
FIGURE 6. Structural comparison of Atg3 with canonical E2s bound to their targets. A, ribbon diagram of Atg3. Color coding is as described in the legend to Fig. 1B. The side chain of Cys-234 and a sulfate ion observed near Cys-234 are shown with stick models. B, ribbon diagram of Ubc12 bound to the Ubl domain of UBA3, a subunit of the E1 for NEDD8 (Protein Data Bank code 1Y8X). Conserved -helices and -strands in Atg3 and Ubc12 are colored red and cyan, respectively. The side chain of Cys-111 is shown with a stick model. C, ribbon diagram of SUMO-RanGAP1 conjugate bound to Ubc9 (Protein Data Bank code 1Z5S). Although Nup358, an E3 enzyme, is also bound to this complex, the protein is not shown in this figure. Gly-97 of SUMO and the side chains of Ubc9 Cys-93 and RanGAP1 Lys-524 are shown with stick models. The figure was prepared using PyMOL. Conserved -helices and -strands in Atg3 and Ubc9 are colored red and cyan, respectively.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2007, 282, 8036-8043) copyright 2007.

Figures were selected by an automated process.