1S1F

Crystal Structure of Streptomyces Coelicolor A3(2) CYP158A2 from antibiotic biosynthetic pathways


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Binding of Two Flaviolin Substrate Molecules, Oxidative Coupling, and Crystal Structure of Streptomyces coelicolor A3(2) Cytochrome P450 158A2

Zhao, B.Guengerich, F.P.Bellamine, A.Lamb, D.C.Izumikawa, M.Lei, L.Podust, L.M.Sundaramoorthy, M.Kalaitzis, J.A.Reddy, L.M.Kelly, S.L.Moore, B.S.Stec, D.Voehler, M.Falck, J.R.Shimada, T.Waterman, M.R.

(2005) J Biol Chem 280: 11599-11607

  • DOI: https://doi.org/10.1074/jbc.M410933200
  • Primary Citation of Related Structures:  
    1S1F, 1SE6, 1T93

  • PubMed Abstract: 

    Cytochrome P450 158A2 (CYP158A2) is encoded within a three-gene operon (sco1206-sco1208) in the prototypic soil bacterium Streptomyces coelicolor A3(2). This operon is widely conserved among streptomycetes. CYP158A2 has been suggested to produce polymers of flaviolin, a pigment that may protect microbes from UV radiation, in combination with the adjacent rppA gene, which encodes the type III polyketide synthase, 1,3,6,8-tetrahydroxynaphthalene synthase. Following cloning, expression, and purification of this cytochrome P450, we have shown that it can produce dimer and trimer products from the substrate flaviolin and that the structures of two of the dimeric products were established using mass spectrometry and multiple NMR methods. A comparison of the x-ray structures of ligand-free (1.75 angstroms) and flaviolin-bound (1.62 angstroms) forms of CYP158A2 demonstrates a major conformational change upon ligand binding that closes the entry into the active site, partly due to repositioning of the F and G helices. Particularly interesting is the presence of two molecules of flaviolin in the closed active site. The flaviolin molecules form a quasi-planar three-molecule stack including the heme of CYP158A2, suggesting that oxidative C-C coupling of these phenolic molecules leads to the production of flaviolin dimers.


  • Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-0146, USA. bin.zhao@vanderbilt.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
putative cytochrome P450406Streptomyces coelicolor A3(2)Mutation(s): 0 
EC: 1.14.19.69
UniProt
Find proteins for Q9FCA6 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Explore Q9FCA6 
Go to UniProtKB:  Q9FCA6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FCA6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
D [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
HG
Query on HG

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N
PIM
Query on PIM

Download Ideal Coordinates CCD File 
E [auth A]4-PHENYL-1H-IMIDAZOLE
C9 H8 N2
XHLKOHSAWQPOFO-UHFFFAOYSA-N
MLA
Query on MLA

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.203 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.25α = 90
b = 65.553β = 90
c = 104.245γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-01-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2015-04-29
    Changes: Non-polymer description
  • Version 1.4: 2017-10-11
    Changes: Refinement description
  • Version 1.5: 2024-02-14
    Changes: Data collection, Database references, Derived calculations