Ferrous dioxygen complex of the A245S cytochrome P450eryF

Experimental Data Snapshot

  • Resolution: 1.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 

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Crystal structures of the ferrous dioxygen complex of wild-type cytochrome P450eryF and its mutants, A245S and A245T: investigation of the proton transfer system in P450eryF.

Nagano, S.Cupp-Vickery, J.R.Poulos, T.L.

(2005) J Biol Chem 280: 22102-22107

  • DOI: https://doi.org/10.1074/jbc.M501732200
  • Primary Citation of Related Structures:  
    1Z8O, 1Z8P, 1Z8Q

  • PubMed Abstract: 

    Cytochrome P450eryF (CYP107A) from Saccaropolyspora ertherea catalyzes the hydroxylation of 6-deoxyerythronolide B, one of the early steps in the biosynthesis of erythromycin. P450eryF has an alanine rather than the conserved threonine that participates in the activation of dioxygen (O(2)) in most other P450s. The initial structure of P450eryF (Cupp-Vickery, J. R., Han, O., Hutchinson, C. R., and Poulos, T. L. (1996) Nat. Struct. Biol. 3, 632-637) suggests that the substrate 5-OH replaces the missing threonine OH group and holds a key active site water molecule in position to donate protons to the iron-linked dioxygen, a critical step for the monooxygenase reaction. To probe the proton delivery system in P450eryF, we have solved crystal structures of ferrous wild-type and mutant (Fe(2+)) dioxygen-bound complexes. The catalytic water molecule that was postulated to provide protons to dioxygen is absent, although the substrate 5-OH group donates a hydrogen bond to the iron-linked dioxygen. The hydrogen bond network observed in the wild-type ferrous dioxygen complex, water 63-Glu(360)-Ser(246)-water 53-Ala(241) carbonyl in the I-helix cleft, is proposed as the proton transfer pathway. Consistent with this view, the hydrogen bond network in the O(2).A245S and O(2) .A245T mutants, which have decreased or no enzyme activity, was perturbed or disrupted, respectively. The mutant Thr(245) side chain also perturbs the hydrogen bond between the substrate 5-OH and dioxygen ligand. Contrary to the previously proposed mechanism, these results support the direct involvement of the substrate in O(2) activation but raise questions on the role water plays as a direct proton donor to the iron-linked dioxygen.

  • Organizational Affiliation

    Departments of Molecular Biology & Biochemistry, Program in Chemical and Structural Biology, University of California-Irvine, Irvine, CA 92697, USA. snagano@riken.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
6-deoxyerythronolide B hydroxylase404Saccharopolyspora erythraeaMutation(s): 1 
Gene Names: eryFCYP107A1
EC: 1
Find proteins for Q00441 (Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338))
Explore Q00441 
Go to UniProtKB:  Q00441
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ00441
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.94α = 90
b = 78.47β = 90
c = 96.79γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-04-12
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-10-20
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-23
    Changes: Data collection, Refinement description