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 

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
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  • 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