Structure of closed cytochrome P450 EryK

Experimental Data Snapshot

  • Resolution: 1.59 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

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Investigating the Structural Plasticity of a Cytochrome P450: Three-Dimensional Structures of P450 Eryk and Binding to its Physiological Substrate.

Savino, C.Montemiglio, L.C.Sciara, G.Miele, A.E.Kendrew, S.G.Jemth, P.Gianni, S.Vallone, B.

(2009) J Biol Chem 284: 29170

  • DOI: https://doi.org/10.1074/jbc.M109.003590
  • Primary Citation of Related Structures:  
    2JJN, 2JJO, 2WIO

  • PubMed Abstract: 

    Cytochrome P450s are heme-containing proteins that catalyze the oxidative metabolism of many physiological endogenous compounds. Because of their unique oxygen chemistry and their key role in drug and xenobiotic metabolism, particular attention has been devoted in elucidating their mechanism of substrate recognition. In this work, we analyzed the three-dimensional structures of a monomeric cytochrome P450 from Saccharopolyspora erythraea, commonly called EryK, and the binding kinetics to its physiological ligand, erythromycin D. Three different structures of EryK were obtained: two ligand-free forms and one in complex with its substrate. Analysis of the substrate-bound structure revealed the key structural determinants involved in substrate recognition and selectivity. Interestingly, the ligand-free structures of EryK suggested that the protein may explore an open and a closed conformation in the absence of substrate. In an effort to validate this hypothesis and to investigate the energetics between such alternative conformations, we performed stopped-flow absorbance experiments. Data demonstrated that EryK binds erythromycin D via a mechanism involving at least two steps. Contrary to previously characterized cytochrome P450s, analysis of double jump mixing experiments confirmed that this complex scenario arises from a pre-existing equilibrium between the open and closed subpopulations of EryK, rather than from an induced-fit type mechanism.

  • Organizational Affiliation

    CNR Institute of Molecular Biology and Pathology, P.le A. Moro 5, 00185 Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME P450 113A1411Saccharopolyspora erythraeaMutation(s): 2 
EC: 1.14 (PDB Primary Data), (UniProt)
Find proteins for P48635 (Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338))
Explore P48635 
Go to UniProtKB:  P48635
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48635
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.59 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.46α = 90
b = 68.004β = 101.05
c = 57.407γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance