Phosphotriesterase Variant Rev6

Experimental Data Snapshot

  • Resolution: 1.51 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report

This is version 1.4 of the entry. See complete history


The role of protein dynamics in the evolution of new enzyme function.

Campbell, E.Kaltenbach, M.Correy, G.J.Carr, P.D.Porebski, B.T.Livingstone, E.K.Afriat-Jurnou, L.Buckle, A.M.Weik, M.Hollfelder, F.Tokuriki, N.Jackson, C.J.

(2016) Nat Chem Biol 12: 944-950

  • DOI: https://doi.org/10.1038/nchembio.2175
  • Primary Citation of Related Structures:  
    4PBE, 4PBF, 4PCN, 4PCP, 4XAF, 4XAG, 4XAY, 4XAZ, 4XD3, 4XD4, 4XD5, 4XD6

  • PubMed Abstract: 

    Enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. The biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. Here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. Analysis of the structures and dynamics of nine protein variants along this trajectory, and three rationally designed variants, reveals cycles of structural destabilization and repair, evolutionary pressure to 'freeze out' unproductive motions and sampling of distinct conformations with specific catalytic properties in bi-functional intermediates. This work establishes that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phosphotriesterase variant PTE-revR6A,
B [auth G]
333Brevundimonas diminutaMutation(s): 0 
Gene Names: opd
Find proteins for A0A060GPP4 (Brevundimonas diminuta)
Explore A0A060GPP4 
Go to UniProtKB:  A0A060GPP4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A060GPP4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.51 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.638α = 90
b = 85.966β = 90
c = 89.188γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2016-09-07
    Changes: Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-11-15
    Changes: Data collection