Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 105.60 kDa 
• Atom Count: 8407 
• Modelled Residue Count: 889 
• Deposited Residue Count: 910 
• Unique protein chains: 1

1P0X

F393Y mutant heme domain of flavocytochrome P450 BM3

• PDB DOI: 10.2210/pdb1P0X/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Priestia megaterium
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-04-11 Released: 2003-12-09 
• Deposition Author(s): Ost, T.W.B., Clark, J., Miles, C.S., Walkinshaw, M.D., Reid, G.A., Chapman, S.K., Daff, S., Mowat, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.172 

Literature

Oxygen Activation and Electron Transfer in Flavocytochrome P450 BM3

Ost, T.W.B., Clark, J., Mowat, C.G., Miles, C.S., Walkinshaw, M.D., Reid, G.A., Chapman, S.K., Daff, S.

(2003) J Am Chem Soc 125: 15010-15020

• PubMed: 14653735 
• DOI: 10.1021/ja035731o
• Primary Citation of Related Structures:  
  1P0V, 1P0W, 1P0X


• PubMed Abstract: 
  

In flavocytochrome P450 BM3, there is a conserved phenylalanine residue at position 393 (Phe393), close to Cys400, the thiolate ligand to the heme. Substitution of Phe393 by Ala, His, Tyr, and Trp has allowed us to modulate the reduction potential of the heme, while retaining the structural integrity of the enzyme's active site. Substrate binding triggers electron transfer in P450 BM3 by inducing a shift from a low- to high-spin ferric heme and a 140 mV increase in the heme reduction potential. Kinetic analysis of the mutants indicated that the spin-state shift alone accelerates the rate of heme reduction (the rate determining step for overall catalysis) by 200-fold and that the concomitant shift in reduction potential is only responsible for a modest 2-fold rate enhancement. The second step in the P450 catalytic cycle involves binding of dioxygen to the ferrous heme. The stabilities of the oxy-ferrous complexes in the mutant enzymes were also analyzed using stopped-flow kinetics. These were found to be surprisingly stable, decaying to superoxide and ferric heme at rates of 0.01-0.5 s(-)(1). The stability of the oxy-ferrous complexes was greater for mutants with higher reduction potentials, which had lower catalytic turnover rates but faster heme reduction rates. The catalytic rate-determining step of these enzymes can no longer be the initial heme reduction event but is likely to be either reduction of the stabilized oxy-ferrous complex, i.e., the second flavin to heme electron transfer or a subsequent protonation event. Modulating the reduction potential of P450 BM3 appears to tune the two steps in opposite directions; the potential of the wild-type enzyme appears to be optimized to maximize the overall rate of turnover. The dependence of the visible absorption spectrum of the oxy-ferrous complex on the heme reduction potential is also discussed.

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Organizational Affiliation: 

School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bifunctional P-450:NADPH-P450 reductase	A, B	455	Priestia megaterium	Mutation(s): 1  Gene Names: CYP102A21 EC: 1.14.14.1 (PDB Primary Data), 1.6.2.4 (UniProt)
UniProt
Find proteins for P14779 (Priestia megaterium (strain ATCC 14581 / DSM 32 / CCUG 1817 / JCM 2506 / NBRC 15308 / NCIMB 9376 / NCTC 10342 / NRRL B-14308 / VKM B-512 / Ford 19)) Explore P14779  Go to UniProtKB:  P14779

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.237 
• R-Value Work: 0.172 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.608	α = 90
b = 152.983	β = 94.54
c = 61.774	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-04-11 
• Released Date: 2003-12-09 
Deposition Author(s): Ost, T.W.B., Clark, J., Miles, C.S., Walkinshaw, M.D., Reid, G.A., Chapman, S.K., Daff, S., Mowat, C.G.

Revision History  

• Version 1.0: 2003-12-09
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-10-27
  Changes: Data collection, Database references, Derived calculations