4FXB

Crystal structure of CYP105N1 from Streptomyces coelicolor: a cytochrome P450 oxidase in the coelibactin siderophore biosynthetic pathway


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.281 

wwPDB Validation 3D Report Full Report


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Literature

Crystal structure of cytochrome P450 CYP105N1 from Streptomyces coelicolor, an oxidase in the coelibactin siderophore biosynthetic pathway

Lim, Y.R.Hong, M.K.Kim, J.K.Doan, T.T.Kim, D.H.Yun, C.H.Chun, Y.J.Kang, L.W.Kim, D.

(2012) Arch.Biochem.Biophys. 528: 111-117

  • DOI: 10.1016/j.abb.2012.09.001

  • PubMed Abstract: 
  • The genome sequence of Streptomyces coelicolor contains 18 cytochrome P450 enzymes. The recombinant CYP105N1 protein has been expressed in Escherichia coli and purified, and we report the biochemical and structural characterization of CYP105N1 from S ...

    The genome sequence of Streptomyces coelicolor contains 18 cytochrome P450 enzymes. The recombinant CYP105N1 protein has been expressed in Escherichia coli and purified, and we report the biochemical and structural characterization of CYP105N1 from S. coelicolor. The purified protein exhibited the typical CO-binding spectrum of P450 enzymes and type I binding spectra with estradiol and a coelibactin analog. The oxidation of estradiol by CYP105N1, supported by H(2)O(2), produced estriol. The crystal structure of CYP105N1 was determined at 2.9 Å resolution. An unexpected wide open binding pocket located above the heme group was identified, with a volume of approximately 4299 Å(3). These results suggest that the large open pocket to the active site may be a key feature for easy access of the peptidyl carrier protein-bound substrate to perform the hydroxylation reaction. A molecular docking model with coelibactin showed that the phenyl group of coelibactin is located <4 Å away from the heme-iron, suggesting that CYP105N1 may be involved in the hydroxylation of the phenyl ring of the coelibactin precursor during biosynthesis.


    Organizational Affiliation

    Department of Biological Sciences, Konkuk University, Seoul, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative cytochrome P450
A, B
417Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)N/A
Find proteins for Q9EWP1 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145))
Go to UniProtKB:  Q9EWP1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download SDF File 
Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.281 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 133.086α = 90.00
b = 133.086β = 90.00
c = 227.111γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
PHASESphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-14
    Type: Initial release