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 
  • R-Value Observed: 0.105 

wwPDB Validation 3D Report Full Report



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:  
    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 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: 

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, 94158, USA. jfraser@fraserlab.com.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase AA165Homo sapiensMutation(s): 3 
Gene Names: PPIA, CYPA
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937
GTEx  ENSG00000196262
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.43 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.104 
  • R-Value Observed: 0.105 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.015α = 90
b = 52.432β = 90
c = 89.246γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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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