4TMB

CRYSTAL STRUCTURE of OLD YELLOW ENZYME from CANDIDA MACEDONIENSIS AKU4588


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

An Engineered Old Yellow Enzyme that Enables Efficient Synthesis of (4R,6R)-Actinol in a One-Pot Reduction System

Horita, S.Kataoka, M.Kitamura, N.Nakagawa, T.Miyakawa, T.Ohtsuka, J.Nagata, K.Shimizu, S.Tanokura, M.

(2015) Chembiochem 16: 440-445

  • DOI: https://doi.org/10.1002/cbic.201402555
  • Primary Citation of Related Structures:  
    4TMB, 4TMC

  • PubMed Abstract: 

    (4R,6R)-Actinol can be stereo-selectively synthesized from ketoisophorone by a two-step conversion using a mixture of two enzymes: Candida macedoniensis old yellow enzyme (CmOYE) and Corynebacterium aquaticum (6R)-levodione reductase. However, (4S)-phorenol, an intermediate, accumulates because of the limited substrate range of CmOYE. To address this issue, we solved crystal structures of CmOYE in the presence and absence of a substrate analogue p-HBA, and introduced point mutations into the substrate-recognition loop. The most effective mutant (P295G) showed two- and 12-fold higher catalytic activities toward ketoisophorone and (4S)-phorenol, respectively, than the wild-type, and improved the yield of the two-step conversion from 67.2 to 90.1%. Our results demonstrate that the substrate range of an enzyme can be changed by introducing mutation(s) into a substrate-recognition loop. This method can be applied to the development of other favorable OYEs with different substrate preferences.


  • Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 (Japan).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Old yellow enzyme
A, B, C, D
403Kluyveromyces marxianusMutation(s): 0 
Gene Names: oye
UniProt
Find proteins for Q6I7B7 (Kluyveromyces marxianus)
Explore Q6I7B7 
Go to UniProtKB:  Q6I7B7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6I7B7
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 287.51α = 90
b = 59.62β = 109.89
c = 100.29γ = 90
Software Package:
Software NamePurpose
PHASERmodel building
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Ministry of Education, Culture, Sports, Science, and Technology of JapanJapan--
National Project on Protein Structural and Functional AnalysesJapan--
the Targeted Proteins Research Program, the Platform for Drug Discovery, Informatics, and Structural Life SciencesJapan--
--

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-11
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Data collection, Derived calculations, Source and taxonomy
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description