CypA Mutant - S99T C115S

Experimental Data Snapshot

  • Resolution: 1.50 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 

wwPDB Validation   3D Report Full Report

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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: https://doi.org/10.1038/s41467-018-03562-9
  • Primary Citation of Related Structures:  
    5WC7, 6BTA

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase A165Homo sapiensMutation(s): 2 
Gene Names: PPIACYPA
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
PHAROS:  P62937
GTEx:  ENSG00000196262 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62937
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.50 Å
  • R-Value Free: 0.146 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.132 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.97α = 90
b = 52.54β = 90
c = 89.27γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-18
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Advisory, Data collection, Database references, Refinement description