3E0L

Computationally Designed Ammelide Deaminase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Alteration of enzyme specificity by computational loop remodeling and design.

Murphy, P.M.Bolduc, J.M.Gallaher, J.L.Stoddard, B.L.Baker, D.

(2009) Proc Natl Acad Sci U S A 106: 9215-9220

  • DOI: https://doi.org/10.1073/pnas.0811070106
  • Primary Citation of Related Structures:  
    3E0L

  • PubMed Abstract: 

    Altering the specificity of an enzyme requires precise positioning of side-chain functional groups that interact with the modified groups of the new substrate. This requires not only sequence changes that introduce the new functional groups but also sequence changes that remodel the structure of the protein backbone so that the functional groups are properly positioned. We describe a computational design method for introducing specific enzyme-substrate interactions by directed remodeling of loops near the active site. Benchmark tests on 8 native protein-ligand complexes show that the method can recover native loop lengths and, often, native loop conformations. We then use the method to redesign a critical loop in human guanine deaminase such that a key side-chain interaction is made with the substrate ammelide. The redesigned enzyme is 100-fold more active on ammelide and 2.5e4-fold less active on guanine than wild-type enzyme: The net change in specificity is 2.5e6-fold. The structure of the designed protein was confirmed by X-ray crystallographic analysis: The remodeled loop adopts a conformation that is within 1-A Calpha RMSD of the computational model.


  • Organizational Affiliation

    Department of Biochemistry, Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine deaminase
A, B
455Homo sapiensMutation(s): 0 
Gene Names: GDA
EC: 3.5.4.3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2T3 (Homo sapiens)
Explore Q9Y2T3 
Go to UniProtKB:  Q9Y2T3
PHAROS:  Q9Y2T3
GTEx:  ENSG00000119125 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y2T3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.205 
  • Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.827α = 90
b = 107.315β = 90
c = 233.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description
  • Version 1.3: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description