7L0I

Ligand-free YopH G352T

Summary for 7L0I

• Entry DOI: 10.2210/pdb7l0i/pdb
• Descriptor: Protein-tyrosine-phosphatase, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID (3 entities in total)
• Functional Keywords: protein tyrosine phosphatase, hydrolase
• Biological source: Yersinia pestis
• Total number of polymer chains: 1
• Total formula weight: 33836.24

Authors

Shen, R.D.,Hengge, A.C.,Johnson, S.J. (deposition date: 2020-12-11, release date: 2021-05-12, Last modification date: 2023-10-18)

Primary citation

Shen, R.,Crean, R.M.,Johnson, S.J.,Kamerlin, S.C.L.,Hengge, A.C.
Single Residue on the WPD-Loop Affects the pH Dependency of Catalysis in Protein Tyrosine Phosphatases.
Jacs Au, 1:646-659, 2021

PubMed Abstract: Catalysis by protein tyrosine phosphatases (PTPs) relies on the motion of a flexible protein loop (the WPD-loop) that carries a residue acting as a general acid/base catalyst during the PTP-catalyzed reaction. The orthogonal substitutions of a noncatalytic residue in the WPD-loops of YopH and PTP1B result in shifted pH-rate profiles from an altered kinetic p of the nucleophilic cysteine. Compared to wild type, the G352T YopH variant has a broadened pH-rate profile, similar activity at optimal pH, but significantly higher activity at low pH. Changes in the corresponding PTP1B T177G variant are more modest and in the opposite direction, with a narrowed pH profile and less activity in the most acidic range. Crystal structures of the variants show no structural perturbations but suggest an increased preference for the WPD-loop-closed conformation. Computational analysis confirms a shift in loop conformational equilibrium in favor of the closed conformation, arising from a combination of increased stability of the closed state and destabilization of the loop-open state. Simulations identify the origins of this population shift, revealing differences in the flexibility of the WPD-loop and neighboring regions. Our results demonstrate that changes to the pH dependency of catalysis by PTPs can result from small changes in amino acid composition in their WPD-loops affecting only loop dynamics and conformational equilibrium. The perturbation of kinetic p values of catalytic residues by nonchemical processes affords a means for nature to alter an enzyme's pH dependency by a less disruptive path than altering electrostatic networks around catalytic residues themselves.

PubMed: 34308419
DOI: 10.1021/jacsau.1c00054

Experimental method

X-RAY DIFFRACTION (2.02 Å)