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PDBsum entry 2dyt
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References listed in PDB file
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Key reference
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Title
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The crystal structure of atg3, An autophagy-Related ubiquitin carrier protein (e2) enzyme that mediates atg8 lipidation.
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Authors
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Y.Yamada,
N.N.Suzuki,
T.Hanada,
Y.Ichimura,
H.Kumeta,
Y.Fujioka,
Y.Ohsumi,
F.Inagaki.
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Ref.
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J Biol Chem, 2007,
282,
8036-8043.
[DOI no: ]
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PubMed id
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Abstract
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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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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).
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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.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2007,
282,
8036-8043)
copyright 2007.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray analysis of atg3.
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Authors
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Y.Yamada,
N.N.Suzuki,
Y.Fujioka,
Y.Ichimura,
Y.Ohsumi,
F.Inagaki.
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Ref.
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Acta Crystallogr Sect F Struct Biol Cryst Commun, 2006,
62,
1016-1017.
[DOI no: ]
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PubMed id
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Figure 1.
A crystal of Atg3. The black scale bar is 100 [micro]m in
length. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2006
October 1; 62(Pt 10): 1016–1017. Published online 2006
September 30. doi: 10.1107/S1744309106036098. Copyright
[copyright] International Union of Crystallography 2006
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The above figure is
reproduced from the cited reference
which is an Open Access publication published by the IUCr
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