Structural and biochemical analysis of atypically low dephosphorylating activity of human dual-specificity phosphatase 28.

Bonsu Ku,Seong Eon Ryu,Won Hong,Seung Jun Kim,Myeongbin Kim,Jae Hoon Kim,Ho-Chul Shin,Chae Won Keum,Donghwan Jeon,Hyunyeol Ryu,Wenqing Xu

doi:10.1371/journal.pone.0187701

Abstract

Dual-specificity phosphatases (DUSPs) constitute a subfamily of protein tyrosine phosphatases, and are intimately involved in the regulation of diverse parameters of cellular signaling and essential biological processes. DUSP28 is one of the DUSP subfamily members that is known to be implicated in the progression of hepatocellular and pancreatic cancers, and its biological functions and enzymatic characteristics are mostly unknown. Herein, we present the crystal structure of human DUSP28 determined to 2.1 Å resolution. DUSP28 adopts a typical DUSP fold, which is composed of a central β-sheet covered by α-helices on both sides and contains a well-ordered activation loop, as do other enzymatically active DUSP proteins. The catalytic pocket of DUSP28, however, appears hardly accessible to a substrate because of the presence of nonconserved bulky residues in the protein tyrosine phosphatase signature motif. Accordingly, DUSP28 showed an atypically low phosphatase activity in the biochemical assay, which was remarkably improved by mutations of two nonconserved residues in the activation loop. Overall, this work reports the structural and biochemical basis for understanding a putative oncological therapeutic target, DUSP28, and also provides a unique mechanism for the regulation of enzymatic activity in the DUSP subfamily proteins.

Highlights

Protein tyrosine phosphorylation is one of the common and critical post-translational modifications that is controlled by coordination of members of two large protein families, protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) [1]
An asymmetric unit of the crystal contains two molecules of DUSP28, which are designated as molecules A and B in S1A Fig. Among all the 176 residues of human DUSP28, residues 12−159 of molecule A and residues 19 −161 of molecule B are visible in the structure
Because molecules A and B overlap each other fairly well when superposed with a root mean square deviation (RMSD) of 0.44 Å over 141 aligned residues, we used the crystal structure of molecule A as a template for the structural analysis of human DUSP28 described below

Summary

Introduction

Protein tyrosine phosphorylation is one of the common and critical post-translational modifications that is controlled by coordination of members of two large protein families, protein tyrosine kinases (PTKs) and protein tyrosine phosphatases (PTPs) [1]. More than 100 PTPs have been reported to be encoded in the human genome [2]. A large proportion of these PTPs has been shown to dephosphorylate phosphorylated tyrosine and other substrates such as phosphorylated serine and threonine or phosphoinositides [1,2]. Crystal structure of human DUSP28 collection and analysis, decision to publish, or preparation of the manuscript

Methods

Results

Conclusion