1SKX

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

Summary for 1SKX

• Entry DOI: 10.2210/pdb1skx/pdb
• Related: 1ILG 1M13
• Descriptor: Orphan nuclear receptor PXR, RIFAMPICIN (3 entities in total)
• Functional Keywords: pregnane x receptor, rifampicin, nuclear receptor, ligand binding domain, transcription
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus: O75469
• Total number of polymer chains: 1
• Total formula weight: 36858.58

Authors

Chrencik, J.E.,Xue, Y.,Orans, J.O.,Redinbo, M.R. (deposition date: 2004-03-05, release date: 2005-03-08, Last modification date: 2023-08-23)

Primary citation

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.
Structural disorder in the complex of human pregnane x receptor and the macrolide antibiotic rifampicin
Mol.Endocrinol., 19:1125-1134, 2005

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. 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.

PubMed: 15705662
DOI: 10.1210/me.2004-0346

Experimental method

X-RAY DIFFRACTION (2.8 Å)