5KYE

Crystal structure of USP7 catalytic domain [H294E] mutant in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Selectively Modulating Conformational States of USP7 Catalytic Domain for Activation.

Ozen, A.Rouge, L.Bashore, C.Hearn, B.R.Skelton, N.J.Dueber, E.C.

(2018) Structure 26: 72-84.e7

  • DOI: 10.1016/j.str.2017.11.010
  • Primary Citation of Related Structures:  

  • 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 c ...

    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.


    Organizational Affiliation

    Department of Pharmaceutical Chemistry and Small Molecule Discovery Center, University of California, San Francisco, San Francisco, CA 94618, USA.,Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA 94080, USA.,Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA 94080, USA; Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA 94080, USA.,Department of Discovery Chemistry, Genentech Inc., South San Francisco, CA 94080, USA. Electronic address: skelton.nick@gene.com.,Department of Structural Biology, Genentech Inc., South San Francisco, CA 94080, USA.,Department of Early Discovery Biochemistry, Genentech Inc., South San Francisco, CA 94080, USA. Electronic address: dueber.erin@gene.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 7
A, B
351Homo sapiensMutation(s): 1 
Gene Names: USP7 (HAUSP)
EC: 3.4.19.12
Find proteins for Q93009 (Homo sapiens)
Go to Gene View: USP7
Go to UniProtKB:  Q93009
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
D, C
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

Download SDF File 
Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.180 
  • Space Group: P 43
Unit Cell:
Length (Å)Angle (°)
a = 99.550α = 90.00
b = 99.550β = 90.00
c = 83.770γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-21 
  • Released Date: 2017-08-09 
  • Deposition Author(s): Rouge, L., Ozen, A.

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Data collection, Database references