6ERA | pdb_00006era

Crystal structure of cyclohexanone monooxygenase mutant (F249A, F280A and F435A) from Rhodococcus sp. Phi1 bound to NADP+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 
    0.262 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.214 (Depositor) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Biocatalytic Routes to Lactone Monomers for Polymer Production.

Messiha, H.L.Ahmed, S.T.Karuppiah, V.Suardiaz, R.Ascue Avalos, G.A.Fey, N.Yeates, S.Toogood, H.S.Mulholland, A.J.Scrutton, N.S.

(2018) Biochemistry 57: 1997-2008

  • DOI: https://doi.org/10.1021/acs.biochem.8b00169
  • Primary Citation Related Structures: 
    6ER9, 6ERA

  • PubMed Abstract: 

    Monoterpenoids offer potential as biocatalytically derived monomer feedstocks for high-performance renewable polymers. We describe a biocatalytic route to lactone monomers menthide and dihydrocarvide employing Baeyer-Villiger monooxygenases (BVMOs) from Pseudomonas sp. HI-70 (CPDMO) and Rhodococcus sp. Phi1 (CHMO Phi1 ) as an alternative to organic synthesis. The regioselectivity of dihydrocarvide isomer formation was controlled by site-directed mutagenesis of three key active site residues in CHMO Phi1 . A combination of crystal structure determination, molecular dynamics simulations, and mechanistic modeling using density functional theory on a range of models provides insight into the origins of the discrimination of the wild type and a variant CHMO Phi1 for producing different regioisomers of the lactone product. Ring-opening polymerizations of the resultant lactones using mild metal-organic catalysts demonstrate their utility in polymer production. This semisynthetic approach utilizing a biocatalytic step, non-petroleum feedstocks, and mild polymerization catalysts allows access to known and also to previously unreported and potentially novel lactone monomers and polymers.


  • Organizational Affiliation
    • Centre for Computational Chemistry, School of Chemistry , University of Bristol , Cantock's Close , Bristol BS8 1TS , U.K.

Macromolecule Content 

  • Total Structure Weight: 124.48 kDa 
  • Atom Count: 8,525 
  • Modeled Residue Count: 1,046 
  • Deposited Residue Count: 1,098 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cyclohexanone monooxygenase
A, B
549Rhodococcus sp. Phi1Mutation(s): 3 
Gene Names: chnB
UniProt
Find proteins for Q84H73 (Rhodococcus sp. Phi1)
Explore Q84H73 
Go to UniProtKB:  Q84H73
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ84H73
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free:  0.262 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.214 (Depositor) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.86α = 90
b = 64.94β = 97.03
c = 187.59γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited KingdomEP/M013219/1

Revision History  (Full details and data files)

  • Version 1.0: 2018-09-26
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary