This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.105.080259v1 91/3/948    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Hu, X. Articles by Stebbins, C. E. Search for Related Content PubMed PubMed Citation Articles by Hu, X. Articles by Stebbins, C. E.

Dynamics of the WPD Loop of the Yersinia Protein Tyrosine Phosphatase

Laboratory of Structural Microbiology, The Rockefeller University, New York, New York 10021

Correspondence: Address reprint requests to C. Erec Stebbins, Tel.: 212-327-7190; Fax: 212-327-7191; E-mail: stebbins{at}rockefeller.edu

The bacterial protein tyrosine phosphatase YopH is an essential virulence determinant in Yersinia spp., causing gastrointestinal diseases and the plague. Like eukaryotic PTPases, YopH catalyzes the hydrolysis of the phosphate moiety of phosphotyrosine within a highly conserved binding pocket, which is also characterized by the closure of the so-called "WPD loop" upon ligand binding. In this study, we investigate the conformational changes and dynamics of the WPD loop by molecular dynamics simulations. Consistent with experimental observations, our simulations show that the WPD loop of YopH is intrinsically flexible and fluctuates between the open and closed conformation with a frequency of 4 ns for the apo, native protein. The region of helix 4 spanning loop 384-392, which has been revealed experimentally as a second substrate-binding site in YopH, is found to be highly associated with the WPD loop, stabilizing it in the closed, active conformation, and providing a structural basis for the cooperation of the second-substrate binding site in substrate recognition. Loop L4 (residues 323–327) is shown to be involved in a parallel, correlated motion mode with the WPD loop that contributes the stabilization of a more extended open conformation. In addition, we have simulated the loop reopening in the ligand-bound protein complex by applying the locally enhanced sampling method. Finally, the dynamic behavior of the WPD loop for the C403S mutant differs from the wild-type YopH remarkably. These results shed light on the role of the WPD loop in PTPase-mediated catalysis, and are useful in structure-based design for novel, selective YopH inhibitors as antibacterial drugs.

This article has been cited by other articles:

				Md. I. Hossain, H. Iwasaki, Y. Okochi, M. Chahine, S. Higashijima, K. Nagayama, and Y. Okamura Enzyme Domain Affects the Movement of the Voltage Sensor in Ascidian and Zebrafish Voltage-sensing Phosphatases J. Biol. Chem., June 27, 2008; 283(26): 18248 - 18259. [Abstract] [Full Text] [PDF]