PDBsum entry 1ukf

Hydrolase

PDB id: 1ukf

Contents

Protein chain

188 a.a. *

Waters ×197

* Residue conservation analysis

PDB id:

1ukf

Name:

Hydrolase

Title:

Crystal structure of pseudomonas avirulence protein avrpphb

Structure:

Avirulence protein avrpph3. Chain: a. Fragment: residues 81-267. Synonym: pseudomonas avrpphb. Engineered: yes

Source:

Pseudomonas syringae pv. Phaseolicola. Organism_taxid: 319. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.35Å R-factor: 0.204 R-free: 0.222

Authors:

M.Zhu,F.Shao,R.W.Innes,J.E.Dixon,Z.Xu

Key ref:

M.Zhu et al. (2004). The crystal structure of Pseudomonas avirulence protein AvrPphB: a papain-like fold with a distinct substrate-binding site. Proc Natl Acad Sci U S A, 101, 302-307. PubMed id: 14694194 DOI: 10.1073/pnas.2036536100

Date:

21-Aug-03 Release date: 09-Dec-03

Protein chain

Q52430  (AVRP3_PSESH) -  Cysteine protease avirulence protein AvrPphB from Pseudomonas savastanoi pv. phaseolicola

Seq: 267 a.a.

Struc: 188 a.a.

Enzyme reactions

• Enzyme class: E.C.3.4.22.- - ?????

DOI no: 10.1073/pnas.2036536100

Proc Natl Acad Sci U S A 101:302-307 (2004)

PubMed id: 14694194

The crystal structure of Pseudomonas avirulence protein AvrPphB: a papain-like fold with a distinct substrate-binding site.

M.Zhu, F.Shao, R.W.Innes, J.E.Dixon, Z.Xu.

ABSTRACT

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.

Selected figure(s)

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.

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).

Figures were selected by an automated process.