4D04 | pdb_00004d04

Structure of the Cys65Asp mutant of phenylacetone monooxygenase: reduced state

• PDB DOI: https://doi.org/10.2210/pdb4D04/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Thermobifida fusca
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 2014-04-24 Released: 2014-12-10 
• Deposition Author(s): Brondani, P.B., Dudek, H.M., Martinoli, C., Mattevi, A., Fraaije, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.216 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Finding the Switch: Turning a Baeyer-Villiger Monooxygenase Into a Nadph Oxidase.

Brondani, P.B., Dudek, H.M., Martinoli, C., Mattevi, A., Fraaije, M.W.

(2014) J Am Chem Soc 136: 16966

• PubMed: 25423359 
• DOI: https://doi.org/10.1021/ja508265b
• Primary Citation Related Structures: 
  4D03, 4D04


• PubMed Abstract: 
  

  By a targeted enzyme engineering approach, we were able to create an efficient NADPH oxidase from a monooxygenase. Intriguingly, replacement of only one specific single amino acid was sufficient for such a monooxygenase-to-oxidase switch-a complete transition in enzyme activity. Pre-steady-state kinetic analysis and elucidation of the crystal structure of the C65D PAMO mutant revealed that the mutation introduces small changes near the flavin cofactor, resulting in a rapid decay of the peroxyflavin intermediate. The engineered biocatalyst was shown to be a thermostable, solvent tolerant, and effective cofactor-regenerating biocatalyst. Therefore, it represents a valuable new biocatalytic tool.

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Organizational Affiliation: 
• Molecular Enzymology Group, University of Groningen , Nijenborgh 4, 9747AG Groningen, The Netherlands.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 63.3 kDa 
• Atom Count: 4,678 
• Modeled Residue Count: 532 
• Deposited Residue Count: 542 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHENYLACETONE MONOOXYGENASE	A	542	Thermobifida fusca	Mutation(s): 1  EC: 1.14.13.92
UniProt
Find proteins for Q47PU3 (Thermobifida fusca (strain YX)) Explore Q47PU3  Go to UniProtKB:  Q47PU3

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP	C [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
P6G	D [auth A], E [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.216 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 107.879	α = 90
b = 107.879	β = 90
c = 107.044	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-10 
Deposition Author(s): Brondani, P.B., Dudek, H.M., Martinoli, C., Mattevi, A., Fraaije, M.W.

Revision History  

• Version 1.0: 2014-12-10
  Type: Initial release
  
• Version 1.1: 2014-12-24
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description