3UCL

Cyclohexanone-bound crystal structure of cyclohexanone monooxygenase in the Rotated conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.198 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

The Substrate-Bound Crystal Structure of a Baeyer-Villiger Monooxygenase Exhibits a Criegee-like Conformation.

Yachnin, B.J.Sprules, T.McEvoy, M.B.Lau, P.C.Berghuis, A.M.

(2012) J Am Chem Soc 134: 7788-7795

  • DOI: https://doi.org/10.1021/ja211876p
  • Primary Citation of Related Structures:  
    3UCL

  • PubMed Abstract: 

    The Baeyer-Villiger monooxygenases (BVMOs) are a family of bacterial flavoproteins that catalyze the synthetically useful Baeyer-Villiger oxidation reaction. This involves the conversion of ketones into esters or cyclic ketones into lactones by introducing an oxygen atom adjacent to the carbonyl group. The BVMOs offer exquisite regio- and enantiospecificity while acting on a wide range of substrates. They use only NADPH and oxygen as cosubstrates, and produce only NADP(+) and water as byproducts, making them environmentally attractive for industrial purposes. Here, we report the first crystal structure of a BVMO, cyclohexanone monooxygenase (CHMO) from Rhodococcus sp. HI-31 in complex with its substrate, cyclohexanone, as well as NADP(+) and FAD, to 2.4 Å resolution. This structure shows a drastic rotation of the NADP(+) cofactor in comparison to previously reported NADP(+)-bound structures, as the nicotinamide moiety is no longer positioned above the flavin ring. Instead, the substrate, cyclohexanone, is found at this location, in an appropriate position for the formation of the Criegee intermediate. The rotation of NADP(+) permits the substrate to gain access to the reactive flavin peroxyanion intermediate while preventing it from diffusing out of the active site. The structure thus reveals the conformation of the enzyme during the key catalytic step. CHMO is proposed to undergo a series of conformational changes to gradually move the substrate from the solvent, via binding in a solvent excluded pocket that dictates the enzyme's chemospecificity, to a location above the flavin-peroxide adduct where catalysis occurs.


  • Organizational Affiliation

    Department of Biochemistry, McGill University, 3649 Promenade Sir William Osler, Bellini Pavilion, Room 466, Montreal, QC, Canada H3G 0B1.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cyclohexanone monooxygenase573Rhodococcus sp. HI-31Mutation(s): 0 
Gene Names: chnBchnB1
EC: 1.14.13.22
UniProt
Find proteins for C0STX7 (Rhodococcus sp. HI-31)
Explore C0STX7 
Go to UniProtKB:  C0STX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC0STX7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.538α = 90
b = 67.105β = 90
c = 131.409γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-25
    Type: Initial release
  • Version 1.1: 2012-05-23
    Changes: Database references
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description