The final, formatted version of the article will be published soon.
ORIGINAL RESEARCH article
Front. Chem. Biol.
Sec. Molecular Sciences
Volume 3 - 2024 |
doi: 10.3389/fchbi.2024.1385560
This article is part of the Research Topic Structure-function relationship of enzymes through a chemical lens View all 5 articles
Structural and Kinetic Characterization of DUSP5 with a Di-Phosphorylated Tripeptide substrate from the ERK Activation Loop
Provisionally accepted- 1 Concordia University (Wisconsin), Mequon, Wisconsin, United States
- 2 School of Medicine, University of Washington, Seattle, Washington, United States
- 3 Medical College of Wisconsin, Milwaukee, Wisconsin, United States
- 4 Colorado State University, Fort Collins, Colorado, United States
- 5 New Mexico State University, Las Cruces, New Mexico, United States
Dual specific phosphatases (DUSPs) are mitogen-activated protein kinase (MAPK) regulators, which also serve as drug targets for treating various vascular diseases. Previously, we have presented mechanistic characterizations of DUSP5 and its interaction with pERK, proposing a dual active site. Herein, we characterize the interactions between the DUSP5 phosphatase domain and the pT-E-pY activation loop of ERK2, with specific active site assignments. We also report the full NMR chemical shift assignments of DUSP5 that now enable chemical shift perturbation and dynamics studies. Both phosphates of the pT-E-pY tripeptide are dephosphorylated, based on 31 P NMR; but, steady state kinetic studies of the tripeptide both as a substrate and as an inhibitor indicate a preference for binding and dephosphorylation of the phospho-tyrosine before the phospho-threonine. Catalytic efficiency (kcat/Km) is 3.7 M -1 S -1 for T-E-pY vs.1.3 M -1 S -1 for pT-E-Y, although the diphosphorylated peptide (pT-E-pY) is a better substrate than both, with kcat/Km = 18.2 M -1 S -1 . Steady state inhibition studies with the pNPP substrate yields Kis values for the peptide substrates of: 15.8 mM (pT-E-Y), 4.93 mM (T-E-pY), 1.67 mM (pT-E-pY). Steady state inhibition studies with pNPP substrate and with vanadate or phosphate inhibitors indicated competitive inhibition with Kis values of 0.000612 mM (sodium vanadate) and 17.3 mM (sodium phosphate), similar to other Protein Tyrosine Phosphatases with an active site cysteine nucleophile that go through a fivecoordinate high energy transition state or intermediate. Molecular dynamics (MD) studies confirm preferential binding of the diphosphorylated peptide, but with preference for binding the pY over the pT reside in the catalytic site proximal to the Cys263 nucleophile. Based on MD, the monophosphorylated peptide binds tighter if phosphorylated on the Tyr vs. the Thr. And, if the starting pose of the docked diphosphorylated peptide has pT in the catalytic site, it will adjust to have the pY in the catalytic site, suggesting a dynamic shifting of the peptide orientation. 2D 1 H-15 N HSQC chemical shift perturbation studies confirm that DUSP5 with tripeptide bound is in a dynamic state, with extensive exchange broadening observedespecially of catalytic site residues.
Keywords: DUSP5, pERK, phosphatase, regulation, enzyme kinetics, phosphorylated peptide substrates, Dual active site, vanadate
Received: 13 Feb 2024; Accepted: 15 Jul 2024.
Copyright: © 2024 Imhoff, Sweeney, Bongard, Syrlybaeva, Gupta, Carpio, Talipov, Garcia-Keller, Crans, Ramchandran and Sem. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Andrea Imhoff, Concordia University (Wisconsin), Mequon, 53097, Wisconsin, United States
Noreena L. Sweeney, Concordia University (Wisconsin), Mequon, 53097, Wisconsin, United States
Raulia Syrlybaeva, School of Medicine, University of Washington, Seattle, 98195, Washington, United States
Marat Talipov, New Mexico State University, Las Cruces, 88003, New Mexico, United States
Costanza Garcia-Keller, Medical College of Wisconsin, Milwaukee, 53226, Wisconsin, United States
Ramani Ramchandran, Medical College of Wisconsin, Milwaukee, 53226, Wisconsin, United States
Daniel Sem, Concordia University (Wisconsin), Mequon, 53097, Wisconsin, United States
Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.