1Q5D

Epothilone B-bound Cytochrome P450epoK


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of epothilone D-bound, epothilone B-bound, and substrate-free forms of cytochrome P450epoK

Nagano, S.Li, H.Shimizu, H.Nishida, C.Ogura, H.Ortiz de Montellano, P.R.Poulos, T.L.

(2003) J.Biol.Chem. 278: 44886-44893

  • DOI: 10.1074/jbc.M308115200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Epothilones are potential anticancer drugs that stabilize microtubules by binding to tubulin in a manner similar to paclitaxel. Cytochrome P450epoK (P450epoK), a heme containing monooxygenase involved in epothilone biosynthesis in the myxobacterium S ...

    Epothilones are potential anticancer drugs that stabilize microtubules by binding to tubulin in a manner similar to paclitaxel. Cytochrome P450epoK (P450epoK), a heme containing monooxygenase involved in epothilone biosynthesis in the myxobacterium Sorangium cellulosum, catalyzes the epoxidation of epothilones C and D into epothilones A and B, respectively. The 2.10-, 1.93-, and 2.65-A crystal structures reported here for the epothilone D-bound, epothilone B-bound, and substrate-free forms, respectively, are the first crystal structures of an epothilone-binding protein. Although the substrate for P450epoK is the largest of a P450 whose x-ray structure is known, the structural changes along with substrate binding or product release are very minor and the overall fold is similar to other P450s. The epothilones are positioned with the macrolide ring roughly perpendicular to the heme plane and I helix, and the thiazole moiety provides key interactions that very likely are critical in determining substrate specificity. Interestingly, there are strong parallels between the epothilone/P450epoK and paclitaxel/tubulin interactions. Based on structural similarities, a plausible epothilone tubulin-binding mode is proposed.


    Organizational Affiliation

    Department of Molecular Biology & Biochemistry, University of California, Irvine, 92697-3900, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
P450 epoxidase
A
419Sorangium cellulosumMutation(s): 0 
Gene Names: cyp167A1 (epoF, epoK)
EC: 1.14.15.-
Find proteins for Q9KIZ4 (Sorangium cellulosum)
Go to UniProtKB:  Q9KIZ4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPB
Query on EPB

Download SDF File 
Download CCD File 
A
7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE
EPOTHILONE B
C27 H41 N O6 S
QXRSDHAAWVKZLJ-PVYNADRNSA-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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.218 
  • Space Group: P 43 2 2
Unit Cell:
Length (Å)Angle (°)
a = 60.430α = 90.00
b = 60.430β = 90.00
c = 252.840γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-10-28
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-31
    Type: Experimental preparation