5O9D

Crystal structure of R. ruber ADH-A, mutant Y294F, W295A, Y54F, F43H, H39Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Relaxation of nonproductive binding and increased rate of coenzyme release in an alcohol dehydrogenase increases turnover with a nonpreferred alcohol enantiomer.

Hamnevik, E.Enugala, T.R.Maurer, D.Ntuku, S.Oliveira, A.Dobritzsch, D.Widersten, M.

(2017) FEBS J. 284: 3895-3914

  • DOI: 10.1111/febs.14279
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Alcohol dehydrogenase A (ADH-A) from Rhodococcus ruber DSM 44541 is a promising biocatalyst for redox transformations of arylsubstituted sec-alcohols and ketones. The enzyme is stereoselective in the oxidation of 1-phenylethanol with a 300-fold prefe ...

    Alcohol dehydrogenase A (ADH-A) from Rhodococcus ruber DSM 44541 is a promising biocatalyst for redox transformations of arylsubstituted sec-alcohols and ketones. The enzyme is stereoselective in the oxidation of 1-phenylethanol with a 300-fold preference for the (S)-enantiomer. The low catalytic efficiency with (R)-1-phenylethanol has been attributed to nonproductive binding of this substrate at the active site. Aiming to modify the enantioselectivity, to rather favor the (R)-alcohol, and also test the possible involvement of nonproductive substrate binding as a mechanism in substrate discrimination, we performed directed laboratory evolution of ADH-A. Three targeted sites that contribute to the active-site cavity were exposed to saturation mutagenesis in a stepwise manner and the generated variants were selected for improved catalytic activity with (R)-1-phenylethanol. After three subsequent rounds of mutagenesis, selection and structure-function analysis of isolated ADH-A variants, we conclude: (a) W295 has a key role as a structural determinant in the discrimination between (R)- and (S)-1-phenylethanol and a W295A substitution fundamentally changes the stereoselectivity of the protein. One observable effect is a faster rate of NADH release, which changes the rate-limiting step of the catalytic cycle from coenzyme release to hydride transfer. (b) The obtained change in enantiopreference, from the (S)- to the (R)-alcohol, can be partly explained by a shift in the nonproductive substrate-binding modes.


    Organizational Affiliation

    Department of Chemistry - BMC, Uppsala University, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Alcohol dehydrogenase
A, B, C, D
352Rhodococcus sp. M8Mutation(s): 5 
Find proteins for A0A1Q8I6M1 (Rhodococcus sp. M8)
Go to UniProtKB:  A0A1Q8I6M1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B, C, D
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
9ON
Query on 9ON

Download SDF File 
Download CCD File 
A, B, C, D
(2~{S})-2-methylpentanedioic acid
C6 H10 O4
AQYCMVICBNBXNA-BYPYZUCNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 65.492α = 90.00
b = 104.828β = 91.13
c = 109.009γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
xia2data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History 

  • Version 1.0: 2017-10-11
    Type: Initial release
  • Version 1.1: 2017-11-29
    Type: Database references