1SKX

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.287 

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
  • Primary Citation of Related Structures:  
    1SKX

  • 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 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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Orphan nuclear receptor PXR A313Homo sapiensMutation(s): 0 
Gene Names: NR1I2PXR
Find proteins for O75469 (Homo sapiens)
Explore O75469 
Go to UniProtKB:  O75469
NIH Common Fund Data Resources
PHAROS:  O75469
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RFP
Query on RFP

Download Ideal Coordinates CCD File 
A
RIFAMPICIN
C43 H58 N4 O12
JQXXHWHPUNPDRT-WLSIYKJHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RFPEC50:  5600   nM  BindingDB
RFPEC50:  190   nM  BindingDB
RFPEC50:  1100   nM  BindingDB
RFPEC50:  2300   nM  BindingDB
RFPEC50:  2000   nM  BindingDB
RFPEC50:  200   nM  BindingDB
RFPEC50:  3200   nM  BindingDB
RFPEC50:  3500   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.287 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.537α = 90
b = 91.537β = 90
c = 85.504γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
HKL-2000data reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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