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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.USA 106: 9215-9220

  • DOI: 10.1073/pnas.0811070106

  • 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Guanine deaminase
A, B
455Homo sapiensMutation(s): 0 
Gene Names: GDA (KIAA1258)
EC: 3.5.4.3
Find proteins for Q9Y2T3 (Homo sapiens)
Go to Gene View: GDA
Go to UniProtKB:  Q9Y2T3
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.202 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.827α = 90.00
b = 107.315β = 90.00
c = 233.620γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
PHASERphasing
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-10-25
    Type: Refinement description