2D09

A Role for Active Site Water Molecules and Hydroxyl Groups of Substrate for Oxygen Activation in Cytochrome P450 158A2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Role of active site water molecules and substrate hydroxyl groups in oxygen activation by cytochrome P450 158A2: a new mechanism of proton transfer

Zhao, B.Guengerich, F.P.Voehler, M.Waterman, M.R.

(2005) J.Biol.Chem. 280: 42188-42197

  • DOI: 10.1074/jbc.M509220200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • From the x-ray crystal structure of CYP158A2 (Zhao, B., Guengerich, F. P., Bellamine, A., Lamb, D. C., Izumikawa, M., Lei, L., Podust, L. M., Sundaramoorthy, M., Reddy, L. M., Kelly, S. L., Kalaitzis, J. A., Stec, D., Voehler, M., Falck, J. R., Moore ...

    From the x-ray crystal structure of CYP158A2 (Zhao, B., Guengerich, F. P., Bellamine, A., Lamb, D. C., Izumikawa, M., Lei, L., Podust, L. M., Sundaramoorthy, M., Reddy, L. M., Kelly, S. L., Kalaitzis, J. A., Stec, D., Voehler, M., Falck, J. R., Moore, B. S., Shimada, T., and Waterman, M. R. (2005) J. Biol. Chem. 280, 11599-11607), one of 18 cytochrome P450 (CYP) genes in the actinomycete Streptomyces coelicolor, ordered active site water molecules (WAT505, WAT600, and WAT640), and hydroxyl groups of the substrate flaviolin were proposed to participate in proton transfer and oxygen cleavage in this monooxygenase. To probe their roles in catalysis, we have studied the crystal structures of a substrate analogue (2-hydroxy-1,4-naphthoquinone) complex with ferric CYP158A2 (2.15 A) and the flaviolin ferrous dioxygen-bound CYP158A2 complex (1.8 A). Catalytic activity toward 2-hydroxy-1,4-naphthoquinone was approximately 70-fold less than with flaviolin. In the ferrous dioxygen-bound flaviolin complex, the three water molecules in the ferric flaviolin complex still occupy the same positions and form hydrogen bonds to the distal dioxygen atom. These findings suggest that CYP158A2 utilizes substrate hydroxyl groups to stabilize active site water and further assist in the iron-linked dioxygen activation. A continuous hydrogen-bonded water network connecting the active site to the protein surface (bulk solvent) not present in the other two ferrous dioxygen-bound P450 structures (CYP101A1/P450cam and CYP107A1/P450eryF) is proposed to participate in the proton-delivery cascade, leading to dioxygen bond scission. This ferrous-dioxygen structure suggests two classes of P450s based on the pathway of proton transfer, one using the highly conserved threonine in the I-helix (CYP101A1) and the other requiring hydroxyl groups of the substrate molecules either directly transferring protons (CYP107A1) or stabilizing a water pathway for proton transfer (CYP158A2).


    Related Citations: 
    • 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


    Organizational Affiliation

    Department of Biochemistry, Centers for Structural Biology, Vanderbilt University School of Medicine, Nashville, Tennessee 37235, USA. bin.zhao@vanderbilt.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
putative cytochrome P450
A
407Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)Mutation(s): 0 
Gene Names: cyp158a2
EC: 1.14.19.69
Find proteins for Q9FCA6 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  Q9FCA6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

Download SDF File 
Download CCD File 
A
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
FLV
Query on FLV

Download SDF File 
Download CCD File 
A
FLAVIOLIN
2,5,7-TRIHYDROXYNAPHTHOQUINONE
C10 H6 O5
RROPNRTUMVVUED-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
FLVKd: 7300 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.000α = 90.00
b = 70.935β = 90.00
c = 102.950γ = 90.00
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description