5KYD

Crystal structure of USP7 catalytic domain [V302K] mutant in complex with ubiquitin

Summary for 5KYD

• Entry DOI: 10.2210/pdb5kyd/pdb
• Related: 5KYB 5KYC 5KYE 5KYF
• Descriptor: Polyubiquitin-B, Ubiquitin carboxyl-terminal hydrolase 7 (3 entities in total)
• Functional Keywords: usp7 catalytic domain, deubiquitinase, v302k mutant, ubiquitin, hydrolase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 2
• Total formula weight: 49194.76

Authors

Rouge, L.,Ozen, A. (deposition date: 2016-07-21, release date: 2017-08-09, Last modification date: 2024-10-30)

Primary citation

Ozen, A.,Rouge, L.,Bashore, C.,Hearn, B.R.,Skelton, N.J.,Dueber, E.C.
Selectively Modulating Conformational States of USP7 Catalytic Domain for Activation.
Structure, 26:72-84.e7, 2018

PubMed Abstract: Ubiquitin-specific protease 7 (USP7) deubiquitinase activity is controlled by a number of regulatory factors, including stimulation by intramolecular accessory domains. Alone, the USP7 catalytic domain (USP7cd) shows limited activity and apo USP7cd crystal structures reveal a disrupted catalytic triad. By contrast, ubiquitin-conjugated USP7cd structures demonstrate the canonical cysteine protease active-site geometry; however, the structural features of the USP7cd that stabilize the inactive conformation and the mechanism of transition between inactive and active states remain unclear. Here we use comparative structural analyses, molecular dynamics simulations, and in silico sequence re-engineering via directed sampling by RosettaDesign to identify key molecular determinants of USP7cd activation and successfully engineer USP7cd for improved activity. Full kinetic analysis and multiple X-ray crystal structures of our designs indicate that electrostatic interactions in the distal "switching loop" region and local packing in the hydrophobic core mediate subtle but significant conformational changes that modulate USP7cd activation.

PubMed: 29249604
DOI: 10.1016/j.str.2017.11.010

Experimental method

X-RAY DIFFRACTION (1.62 Å)