1SKX

Structural Disorder in the Complex of Human PXR and the Macrolide Antibiotic Rifampicin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural disorder in the complex of human pregnane x receptor and the macrolide antibiotic rifampicin

Chrencik, J.E.Orans, J.O.Moore, L.B.Xue, Y.Peng, L.Collins, J.L.Wisely, G.B.Lambert, M.H.Kliewer, S.A.Redinbo, M.R.

(2005) Mol.Endocrinol. 19: 1125-1134

  • DOI: 10.1210/me.2004-0346

  • PubMed Abstract: 
  • The human nuclear xenobiotic receptor, pregnane X receptor (PXR), detects a variety of structurally distinct endogenous and xenobiotic compounds and controls expression of genes central to drug and cholesterol metabolism. The macrolide antibiotic rif ...

    The human nuclear xenobiotic receptor, pregnane X receptor (PXR), detects a variety of structurally distinct endogenous and xenobiotic compounds and controls expression of genes central to drug and cholesterol metabolism. The macrolide antibiotic rifampicin, a front-line treatment for tuberculosis, is an established PXR agonist and, at 823 Da, is one of the largest known ligands for the receptor. We present the 2.8 A crystal structure of the ligand-binding domain of human PXR in complex with rifampicin. We also use structural and mutagenesis data to examine the origins of the directed promiscuity exhibited by the PXRs across species. Three structurally flexible loops adjacent to the ligand-binding pocket of PXR are disordered in this crystal structure, including the 200-210 region that is part of a sequence insert novel to the promiscuous PXRs relative to other members of the nuclear receptor superfamily. The 4-methyl-1-piperazinyl ring of rifampicin, which would lie adjacent to the disordered protein regions, is also disordered and not observed in the structure. Taken together, our results indicate that one wall of the PXR ligand-binding cavity can remain flexible even when the receptor is in complex with an activating ligand. These observations highlight the key role that structural flexibility plays in PXR's promiscuous response to xenobiotics.


    Organizational Affiliation

    Department of Chemistry, Campus Box 3290, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Orphan nuclear receptor PXR
A
313Homo sapiensMutation(s): 0 
Gene Names: NR1I2 (PXR)
Find proteins for O75469 (Homo sapiens)
Go to Gene View: NR1I2
Go to UniProtKB:  O75469
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RFP
Query on RFP

Download SDF File 
Download CCD File 
A
RIFAMPICIN
C43 H58 N4 O12
JQXXHWHPUNPDRT-WLSIYKJHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.537α = 90.00
b = 91.537β = 90.00
c = 85.504γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
HKL-2000data collection
TRUNCATEdata reduction
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-08
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance