5WC7

CypA Mutant - I97V S99T C115S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.104 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Rescue of conformational dynamics in enzyme catalysis by directed evolution.

Otten, R.Liu, L.Kenner, L.R.Clarkson, M.W.Mavor, D.Tawfik, D.S.Kern, D.Fraser, J.S.

(2018) Nat Commun 9: 1314-1314

  • DOI: 10.1038/s41467-018-03562-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rational design and directed evolution have proved to be successful approaches to increase catalytic efficiencies of both natural and artificial enzymes. Protein dynamics is recognized as important, but due to the inherent flexibility of biological m ...

    Rational design and directed evolution have proved to be successful approaches to increase catalytic efficiencies of both natural and artificial enzymes. Protein dynamics is recognized as important, but due to the inherent flexibility of biological macromolecules it is often difficult to distinguish which conformational changes are directly related to function. Here, we use directed evolution on an impaired mutant of the proline isomerase CypA and identify two second-shell mutations that partially restore its catalytic activity. We show both kinetically, using NMR spectroscopy, and structurally, by room-temperature X-ray crystallography, how local perturbations propagate through a large allosteric network to facilitate conformational dynamics. The increased catalysis selected for in the evolutionary screen is correlated with an accelerated interconversion between the two catalytically essential conformational sub-states, which are both captured in the high-resolution X-ray ensembles. Our data provide a glimpse of an evolutionary trajectory and show how subtle changes can fine-tune enzyme function.


    Organizational Affiliation

    Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA. jfraser@fraserlab.com.,Howard Hughes Medical Institute and Department of Biochemistry, Brandeis University, 415 South Street, Waltham, MA, 02454, USA. dkern@brandeis.edu.,Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA.,Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel.,Biological Sciences West, The University of Arizona, 1041 E Lowell Street, Tucson, AZ, 85721, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase A
A
165Homo sapiensMutation(s): 3 
Gene Names: PPIA (CYPA)
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Go to Gene View: PPIA
Go to UniProtKB:  P62937
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.104 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.015α = 90.00
b = 52.432β = 90.00
c = 89.246γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-06-29 
  • Released Date: 2018-04-18 
  • Deposition Author(s): Fraser, J.S.

Revision History 

  • Version 1.0: 2018-04-18
    Type: Initial release