4RF3

Crystal Structure of ketoreductase from Lactobacillus kefir, mutant A94F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.694 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Origins of stereoselectivity in evolved ketoreductases.

Noey, E.L.Tibrewal, N.Jimenez-Oses, G.Osuna, S.Park, J.Bond, C.M.Cascio, D.Liang, J.Zhang, X.Huisman, G.W.Tang, Y.Houk, K.N.

(2015) Proc.Natl.Acad.Sci.USA 112: E7065-E7072

  • DOI: 10.1073/pnas.1507910112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only th ...

    Mutants of Lactobacillus kefir short-chain alcohol dehydrogenase, used here as ketoreductases (KREDs), enantioselectively reduce the pharmaceutically relevant substrates 3-thiacyclopentanone and 3-oxacyclopentanone. These substrates differ by only the heteroatom (S or O) in the ring, but the KRED mutants reduce them with different enantioselectivities. Kinetic studies show that these enzymes are more efficient with 3-thiacyclopentanone than with 3-oxacyclopentanone. X-ray crystal structures of apo- and NADP(+)-bound selected mutants show that the substrate-binding loop conformational preferences are modified by these mutations. Quantum mechanical calculations and molecular dynamics (MD) simulations are used to investigate the mechanism of reduction by the enzyme. We have developed an MD-based method for studying the diastereomeric transition state complexes and rationalize different enantiomeric ratios. This method, which probes the stability of the catalytic arrangement within the theozyme, shows a correlation between the relative fractions of catalytically competent poses for the enantiomeric reductions and the experimental enantiomeric ratio. Some mutations, such as A94F and Y190F, induce conformational changes in the active site that enlarge the small binding pocket, facilitating accommodation of the larger S atom in this region and enhancing S-selectivity with 3-thiacyclopentanone. In contrast, in the E145S mutant and the final variant evolved for large-scale production of the intermediate for the antibiotic sulopenem, R-selectivity is promoted by shrinking the small binding pocket, thereby destabilizing the pro-S orientation.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADPH dependent R-specific alcohol dehydrogenase
A, B
272Lactobacillus kefiriMutation(s): 1 
Gene Names: adhR
Find proteins for Q6WVP7 (Lactobacillus kefiri)
Go to UniProtKB:  Q6WVP7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.694 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 66.150α = 90.00
b = 110.670β = 90.00
c = 67.610γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2015-11-25
    Type: Database references
  • Version 1.2: 2015-12-23
    Type: Database references
  • Version 1.3: 2016-01-06
    Type: Database references