Crystal structure of E. coli aspartate aminotransferase mutant AIFS in the ligand-free form at 100 K

Experimental Data Snapshot

  • Resolution: 2.18 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 

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This is version 1.2 of the entry. See complete history


Computational remodeling of an enzyme conformational landscape for altered substrate selectivity.

St-Jacques, A.D.Rodriguez, J.M.Eason, M.G.Foster, S.M.Khan, S.T.Damry, A.M.Goto, N.K.Thompson, M.C.Chica, R.A.

(2023) Nat Commun 14: 6058-6058

  • DOI: https://doi.org/10.1038/s41467-023-41762-0
  • Primary Citation of Related Structures:  
    8E9C, 8E9D, 8E9J, 8E9K, 8E9L, 8E9M, 8E9N, 8E9O, 8E9P, 8E9Q, 8E9R, 8E9S, 8E9T, 8E9U, 8E9V

  • PubMed Abstract: 

    Structural plasticity of enzymes dictates their function. Yet, our ability to rationally remodel enzyme conformational landscapes to tailor catalytic properties remains limited. Here, we report a computational procedure for tuning conformational landscapes that is based on multistate design of hinge-mediated domain motions. Using this method, we redesign the conformational landscape of a natural aminotransferase to preferentially stabilize a less populated but reactive conformation and thereby increase catalytic efficiency with a non-native substrate, resulting in altered substrate selectivity. Steady-state kinetics of designed variants reveals activity increases with the non-native substrate of approximately 100-fold and selectivity switches of up to 1900-fold. Structural analyses by room-temperature X-ray crystallography and multitemperature nuclear magnetic resonance spectroscopy confirm that conformational equilibria favor the target conformation. Our computational approach opens the door to targeted alterations of conformational states and equilibria, which should facilitate the design of biocatalysts with customized activity and selectivity.

  • Organizational Affiliation

    Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, K1N 6N5, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aspartate aminotransferase
A, B
406Escherichia coliMutation(s): 4 
Gene Names: aspCb0928JW0911
Find proteins for P00509 (Escherichia coli (strain K12))
Explore P00509 
Go to UniProtKB:  P00509
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00509
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.18 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.193 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.63α = 90
b = 141.63β = 90
c = 80.92γ = 120
Software Package:
Software NamePurpose
xia2data reduction
DIALSdata scaling

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaRGPIN-2016-04831
Ontario Early Researcher AwardsCanadaER14-10-139
Canada Foundation for InnovationCanada26503
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124149
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124169

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-18
    Changes: Refinement description