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PDBsum entry 1ukf
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Contents |
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* Residue conservation analysis
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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 pseudomonas avirulence protein avrpphb: a papain-Like fold with a distinct substrate-Binding site.
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Authors
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M.Zhu,
F.Shao,
R.W.Innes,
J.E.Dixon,
Z.Xu.
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Ref.
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Proc Natl Acad Sci U S A, 2004,
101,
302-307.
[DOI no: ]
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PubMed id
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Abstract
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AvrPphB is an avirulence (Avr) protein from the plant pathogen Pseudomonas
syringae that can trigger a disease-resistance response in a number of host
plants including Arabidopsis. AvrPphB belongs to a novel family of cysteine
proteases with the charter member of this family being the Yersinia effector
protein YopT. AvrPphB has a very stringent substrate specificity, catalyzing a
single proteolytic cleavage in the Arabidopsis serine/threonine kinase PBS1. We
have determined the crystal structure of AvrPphB by x-ray crystallography at
1.35-A resolution. The structure is composed of a central antiparallel
beta-sheet, with alpha-helices packing on both sides of the sheet to form a
two-lobe structure. The core of this structure resembles the papain-like
cysteine proteases. The similarity includes the AvrPphB active site catalytic
triad of Cys-98, His-212, and Asp-227 and the oxyanion hole residue Asn-93.
Based on analogy with inhibitor complexes of the papain-like proteases, we
propose a model for the substrate-binding mechanism of AvrPphB. A deep and
positively charged pocket (S2) and a neighboring shallow surface (S3) likely
bind to aspartic acid and glycine residues in the substrate located two (P2) and
three (P3) residues N terminal to the cleavage site, respectively. Further
implications about the specificity of plant pathogen recognition are also
discussed.
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Figure 3.
Fig. 3. Electron density map of AvrPphB. Stereo pair of a
 [A]-weighed 2|F[o]| -
|F[c]| simulated-annealing omit electron density map (1.35
Å, contoured at 1.2 ) calculated with the
final refined coordinates. Shown here is a region near the
catalytic triad. The region includes highly conserved residues
Trp-105, Asp-227 (one of the catalytic triad residues), Pro-228,
Asn-229, Gly-231, Glu-232, and Phe-233. Notably, the rings of
Trp-105, Phe-226, and Pro-228 are stacked on each other. The
image was prepared with the program MOLSCRIPT.
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Figure 5.
Fig. 5. The structural basis of AvrPphB substrate
specificity. (A) Sequence comparison of AvrPphB cleavage sites
in its precursor and substrate PBS1 protein. A common
Gly-Asp-Lys motif preceding the cleavage sites is highlighted in
red, and the arrow indicates the cleavage sites. (B and C)
Active site clefts of papain-like enzyme and AvrPphB.
Orientation is the same as in Fig. 4A. B shows the molecular
surface of cruzain (PDB ID code 2aim [PDB]
), and C shows that of AvrPphB. The structure of cruzain was
determined with the inhibitor benzoyl-Arg-Ala-fluoromethyl
ketone, which occupies the S3, S2, and S1 sites and is shown in
B Left as a CPK representation. C Right is a zoom-in view of the
proposed active site of AvrPphB. The proposed S2 site residue
(Arg-205) and four catalytically important residues are drawn
underneath the molecular surface. Note the positive character of
S2 and shallowness of S3 at the substrate-binding site. All
surfaces are colored based on the electrostatic potential of the
molecule (ranging from -23 to +23 kT). Images were prepared with
the program GRASP (53).
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