4RG3

Epsilon-caprolactone-bound crystal structure of cyclohexanone monooxygenase in the Tight conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Lactone-bound structures of cyclohexanone monooxygenase provide insight into the stereochemistry of catalysis.

Yachnin, B.J.McEvoy, M.B.MacCuish, R.J.Morley, K.L.Lau, P.C.Berghuis, A.M.

(2014) Acs Chem.Biol. 9: 2843-2851

  • DOI: 10.1021/cb500442e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Baeyer-Villiger monooxygenases (BVMOs) are microbial enzymes that catalyze the synthetically useful Baeyer-Villiger oxidation reaction. The available BVMO crystal structures all lack a substrate or product bound in a position that would determine ...

    The Baeyer-Villiger monooxygenases (BVMOs) are microbial enzymes that catalyze the synthetically useful Baeyer-Villiger oxidation reaction. The available BVMO crystal structures all lack a substrate or product bound in a position that would determine the substrate specificity and stereospecificity of the enzyme. Here, we report two crystal structures of cyclohexanone monooxygenase (CHMO) with its product, ε-caprolactone, bound: the CHMO(Tight) and CHMO(Loose) structures. The CHMO(Tight) structure represents the enzyme state in which substrate acceptance and stereospecificity is determined, providing a foundation for engineering BVMOs with altered substrate spectra and/or stereospecificity. The CHMO(Loose) structure is the first structure where the product is solvent accessible. This structure represents the enzyme state upon binding and release of the substrate and product. In addition, the role of the invariant Arg329 in chaperoning the substrate/product during the catalytic cycle is highlighted. Overall, these data provide a structural framework for the engineering of BVMOs with altered substrate spectra and/or stereospecificity.


    Organizational Affiliation

    Departments of †Biochemistry and ‡Microbiology & Immunology, McGill University , 3649 Promenade Sir William Osler, Bellini Pavilion, Room 466, Montreal, Quebec, Canada H3G 0B1.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cyclohexanone monooxygenase
A
548Rhodococcus sp. HI-31Mutation(s): 0 
Gene Names: chnB
Find proteins for C0STX7 (Rhodococcus sp. HI-31)
Go to UniProtKB:  C0STX7
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ECE
Query on ECE

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Download CCD File 
A
Caprolactone
Oxepan-2-one; Epsilon-Caprolactone
C6 H10 O2
PAPBSGBWRJIAAV-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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Download CCD File 
A
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NAP
Query on NAP

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Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
BCN
Query on BCN

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Download CCD File 
A
BICINE
C6 H13 N O4
FSVCELGFZIQNCK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.698α = 90.00
b = 67.060β = 90.00
c = 131.641γ = 90.00
Software Package:
Software NamePurpose
StructureStudiodata collection
REFMACphasing
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2015-01-14
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description