4YOF

DosS GAFA Domain Reduced Nitric Oxide Bound Crystal Structure

Summary for 4YOF

• Entry DOI: 10.2210/pdb4yof/pdb
• Related: 2W3D 2W3F 4YNR
• Descriptor: Redox sensor histidine kinase response regulator DevS, PROTOPORPHYRIN IX CONTAINING FE, NITRIC OXIDE, ... (4 entities in total)
• Functional Keywords: doss, tuberculosis, heme, gas sensor, oxidoreductase
• Biological source: Mycobacterium tuberculosis (strain CDC 1551 / Oshkosh)
• Total number of polymer chains: 2
• Total formula weight: 34979.13

Authors

Madrona, Y. (deposition date: 2015-03-11, release date: 2016-03-23, Last modification date: 2023-11-29)

Primary citation

Basudhar, D.,Madrona, Y.,Kandel, S.,Lampe, J.N.,Nishida, C.R.,de Montellano, P.R.
Analysis of cytochrome P450 CYP119 ligand-dependent conformational dynamics by two-dimensional NMR and X-ray crystallography.
J.Biol.Chem., 290:10000-10017, 2015

PubMed Abstract: Defining the conformational states of cytochrome P450 active sites is critical for the design of agents that minimize drug-drug interactions, the development of isoform-specific P450 inhibitors, and the engineering of novel oxidative catalysts. We used two-dimensional (1)H,(15)N HSQC chemical shift perturbation mapping of (15)N-labeled Phe residues and x-ray crystallography to examine the ligand-dependent conformational dynamics of CYP119. Active site Phe residues were most affected by the binding of azole inhibitors and fatty acid substrates, in agreement with active site localization of the conformational changes. This was supported by crystallography, which revealed movement of the F-G loop with various azoles. Nevertheless, the NMR chemical shift perturbations caused by azoles and substrates were distinguishable. The absence of significant chemical shift perturbations with several azoles revealed binding of ligands to an open conformation similar to that of the ligand-free state. In contrast, 4-phenylimidazole caused pronounced NMR changes involving Phe-87, Phe-144, and Phe-153 that support the closed conformation found in the crystal structure. The same closed conformation is observed by NMR and crystallography with a para-fluoro substituent on the 4-phenylimidazole, but a para-chloro or bromo substituent engendered a second closed conformation. An open conformation is thus favored in solution with many azole ligands, but para-substituted phenylimidazoles give rise to two closed conformations that depend on the size of the para-substituent. The results suggest that ligands selectively stabilize discrete cytochrome P450 conformational states.

PubMed: 25670859
DOI: 10.1074/jbc.M114.627935

Experimental method

X-RAY DIFFRACTION (1.9 Å)