3G1Q

Crystal structure of sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in ligand free state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of Trypanosoma brucei sterol 14alpha-demethylase and implications for selective treatment of human infections.

Lepesheva, G.I.Park, H.W.Hargrove, T.Y.Vanhollebeke, B.Wawrzak, Z.Harp, J.M.Sundaramoorthy, M.Nes, W.D.Pays, E.Chaudhuri, M.Villalta, F.Waterman, M.R.

(2010) J.Biol.Chem. 285: 1773-1780

  • DOI: 10.1074/jbc.M109.067470
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sterol 14alpha-demethylase (14DM, the CYP51 family of cytochrome P450) is an essential enzyme in sterol biosynthesis in eukaryotes. It serves as a major drug target for fungal diseases and can potentially become a target for treatment of human infect ...

    Sterol 14alpha-demethylase (14DM, the CYP51 family of cytochrome P450) is an essential enzyme in sterol biosynthesis in eukaryotes. It serves as a major drug target for fungal diseases and can potentially become a target for treatment of human infections with protozoa. Here we present 1.9 A resolution crystal structures of 14DM from the protozoan pathogen Trypanosoma brucei, ligand-free and complexed with a strong chemically selected inhibitor N-1-(2,4-dichlorophenyl)-2-(1H-imidazol-1-yl)ethyl)-4-(5-phenyl-1,3,4-oxadi-azol-2-yl)benzamide that we previously found to produce potent antiparasitic effects in Trypanosomatidae. This is the first structure of a eukaryotic microsomal 14DM that acts on sterol biosynthesis, and it differs profoundly from that of the water-soluble CYP51 family member from Mycobacterium tuberculosis, both in organization of the active site cavity and in the substrate access channel location. Inhibitor binding does not cause large scale conformational rearrangements, yet induces unanticipated local alterations in the active site, including formation of a hydrogen bond network that connects, via the inhibitor amide group fragment, two remote functionally essential protein segments and alters the heme environment. The inhibitor binding mode provides a possible explanation for both its functionally irreversible effect on the enzyme activity and its selectivity toward the 14DM from human pathogens versus the human 14DM ortholog. The structures shed new light on 14DM functional conservation and open an excellent opportunity for directed design of novel antiparasitic drugs.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, USA. galina.i.lepesheva@vanderbilt.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sterol 14-alpha-demethylase
A, B, C, D
450Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 5 
EC: 1.14.13.70
Find proteins for Q385E8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q385E8
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.195 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 59.823α = 74.21
b = 79.874β = 81.56
c = 117.146γ = 68.49
Software Package:
Software NamePurpose
SOLVEphasing
HKL-2000data reduction
REFMACrefinement
HKL-2000data scaling
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description