The 1.92 A structure of Streptomyces coelicolor A3(2) CYP154C1: A new monooxygenase that functionalizes macrolide ring systems

Experimental Data Snapshot

  • Resolution: 1.92 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 

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The 1.92 A Structure of Streptomyces Coelicolor A3(2) Cyp154C1: A New Monooxygenase that Functionalizes Macrolide Ring Systems

Podust, L.M.Kim, Y.Arase, M.Neely, B.A.Beck, B.J.Bach, H.Sherman, D.H.Lamb, D.C.Kelly, S.L.Waterman, M.R.

(2003) J Biol Chem 278: 12214

  • DOI: https://doi.org/10.1074/jbc.M212210200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Evolutionary links between cytochrome P450 monooxygenases, a superfamily of extraordinarily divergent heme-thiolate proteins catalyzing a wide array of NADPH/NADH- and O(2)-dependent reactions, are becoming better understood because of availability of an increasing number of fully sequenced genomes. Among other reactions, P450s catalyze the site-specific oxidation of the precursors to macrolide antibiotics in the genus Streptomyces introducing regiochemical diversity into the macrolide ring system, thereby significantly increasing antibiotic activity. Developing effective uses for Streptomyces enzymes in biosynthetic processes and bioremediation requires identification and engineering of additional monooxygenases with activities toward a diverse array of small molecules. To elucidate the molecular basis for substrate specificity of oxidative enzymes toward macrolide antibiotics, the x-ray structure of CYP154C1 from Streptomyces coelicolor A3(2) was determined (Protein Data Bank code ). Relocation of certain common P450 secondary structure elements, along with a novel structural feature involving an additional beta-strand transforming the five-stranded beta-sheet into a six-stranded variant, creates an open cleft-shaped substrate-binding site between the two P450 domains. High sequence similarity to macrolide monooxygenases from other microbial species translates into catalytic activity of CYP154C1 toward both 12- and 14-membered ring macrolactones in vitro.

  • Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA. larissa.m.podust@vanderbilt.edu

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
411Streptomyces coelicolor A3(2)Mutation(s): 0 
Find proteins for Q9L142 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9L142 
Go to UniProtKB:  Q9L142
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9L142
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on HEM

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
C34 H32 Fe N4 O4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
H [auth B],
I [auth B],
J [auth B],
K [auth B]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.92 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.728α = 90
b = 131.973β = 90
c = 134.886γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Refinement description
  • Version 1.4: 2019-05-08
    Changes: Data collection, Experimental preparation
  • Version 1.5: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other