5IT1

Streptomyces peucetius CYP105P2 complex with biphenyl compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure of Cytochrome P450 (CYP105P2) from Streptomyces peucetius and Its Conformational Changes in Response to Substrate Binding

Lee, C.W.Lee, J.H.Rimal, H.Park, H.Lee, J.H.Oh, T.J.

(2016) Int J Mol Sci 17: --

  • DOI: 10.3390/ijms17060813

  • PubMed Abstract: 
  • Cytochrome P450 monooxygenases (CYP, EC 1.14.14.1) belong to a large family of enzymes that catalyze the hydroxylation of various substrates. Here, we present the crystal structure of CYP105P2 isolated from Streptomyces peucetius ATCC27952 at a 2.1 Å ...

    Cytochrome P450 monooxygenases (CYP, EC 1.14.14.1) belong to a large family of enzymes that catalyze the hydroxylation of various substrates. Here, we present the crystal structure of CYP105P2 isolated from Streptomyces peucetius ATCC27952 at a 2.1 Å resolution. The structure shows the presence of a pseudo-ligand molecule in the active site, which was co-purified fortuitously and is presumed to be a biphenyl derivative. Comparison with previously determined substrate-bound CYP structures showed that binding of the ligand produces large and distinctive conformational changes in α2-α3, α7-α9, and the C-terminal loop regions. This structural flexibility confirms our previous observation that CYP105P2 can accommodate a broad range of ligands. The structure complexed with a pseudo-ligand provides the first molecular view of CYP105P2-ligand interactions, and it indicates the involvement of hydrophobic residues (Pro82, Ala181, Met187, Leu189, Leu193, and Ile236) in the interactions between hydrophobic ligands and CYP105P2. These results provide useful insights into the structural changes involved in the recognition of different ligands by CYP105P2.


    Organizational Affiliation

    Division of Polar Life Sciences, Korea Polar Research Institute, Incheon 406-840, Korea. justay@kopri.re.kr.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative cytochrome P450
A, B, C, D
399Streptomyces peucetiusMutation(s): 0 
Gene Names: cyp7863
EC: 1.14.14.1
Find proteins for Q70AS3 (Streptomyces peucetius)
Go to UniProtKB:  Q70AS3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B, C, D
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
2OH
Query on 2OH

Download SDF File 
Download CCD File 
A, B, C, D
4,4'-PROPANE-2,2-DIYLDIPHENOL
4,4'-ISOPROPYLIDENEDIPHENOL, BISPHENOL A
C15 H16 O2
IISBACLAFKSPIT-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.200 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.023α = 90.00
b = 122.941β = 90.03
c = 193.287γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
HKL-2000data processing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-03-16 
  • Released Date: 2016-06-08 
  • Deposition Author(s): Lee, C.W., Lee, J.H.

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Structure summary