Prediction of a ligand‐induced conformational change in the catalytic core of Cdc25A

Abstract

The cell cycle control phosphatases Cdc25 are dual specificity phosphatases that dephosphorylate both phosphothreonine and phosphotyrosine residues on their substrate proteins. The determination of the apo-protein structure of Cdc25A revealed that this enzyme has a completely different fold compared to all other phosphatases crystallised to date. The conformation of the active site residues does not seem very suitable for catalysis in this unliganded structure. We have studied some structural features of the Cdc25A apo-structure and a modelled Cdc25A-ligand complex by molecular dynamics simulations. The simulations predict a conformational change in the peptide backbone of the complex, which is not observed in the apo-structure. This ligand-induced conformational change yields a structure that is similar to other protein tyrosine phosphataseligand complexes that have been crystallised. The change in conformation takes place in the position between a serine and a glutamic acid residue in the phosphate binding loop. We suggest that this type of conformational change is an important molecular switch in the catalytic process.z 2000 Federation of European Biochemical Societies.

Peptide Conformational Equilibria Computed via a Single-Stage Shifting Protocol

“…The results for ∆G are summarized in Table 1 where we used both the lowest energy frame and histogram peak shifting approaches (Section 2.3) to estimate ∆G for leucine dipeptide. The value of ∆S was found to be zero within uncertainty, consistent with the value found using eq (9). For each shifting approach, we tested four sets of shifting coordinates: backbone torsions only, all torsions, all torsions and bond angles, or all internal coordinates (torsions, angles and bond lengths).…”

“…45 The superior convergence properties of the iterative method can be seen in Figure 2. The solid horizontal black line represents the independent, 4.0 µsec ∆G value obtained by using eq (9). The data are ∆G estimates using the singlestage shifting method, where backbone torsions were shifted according to the histogram peaks.…”

The catalytic mechanism of protein tyrosine phosphatases revisited

“…Using the natural substrate the k cat/ K M pH rate profiles also showed a typical slope of −1 on the basic side, often assigned to general acid catalysis. It is also noteworthy that the necessary conformational change for catalysis in cdc25 was correctly predicted by MD simulations [25] as judged from a recent crystal structure [26].…”

Knowledge-Based Characterization of Similarity Relationships in the Human Protein−Tyrosine Phosphatase Family for Rational Inhibitor Design

“…It is not quite clear which residue replaces the aspartic acid from the WPD loop and reacts as a general acid in the catalytic reaction of such PTPs. Some previous studies have shown that the general acid residue perhaps can be a part of the catalytic (H/V)C(X)5R(S/T) loop 49,50. The side chain conformation of such a residue would therefore define an active form for these phosphatases.…”