3R1A

Closed crystal structure of cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene

Summary for 3R1A

• Entry DOI: 10.2210/pdb3r1a/pdb
• Related: 3R1B
• Descriptor: Cytochrome P450 2B4, PROTOPORPHYRIN IX CONTAINING FE, (4-tert-butylphenyl)acetaldehyde, ... (4 entities in total)
• Functional Keywords: cytochrome p450 2b4, monooxygenase, oxidoreductase, membrane protein, t302 covalently linked to tert-butylphenylacetylene, oxidoreductase-oxidoreductase inhibitor complex, oxidoreductase/oxidoreductase inhibitor
• Biological source: Oryctolagus cuniculus (European rabbit,Japanese white rabbit,domestic rabbit,rabbits)
• Cellular location: Endoplasmic reticulum membrane; Peripheral membrane protein: P00178
• Total number of polymer chains: 8
• Total formula weight: 439694.59

Authors

Gay, S.C.,Zhang, H.,Stout, C.D.,Hollenberg, P.F.,Halpert, J.R. (deposition date: 2011-03-09, release date: 2011-05-11, Last modification date: 2024-11-27)

Primary citation

Gay, S.C.,Zhang, H.,Wilderman, P.R.,Roberts, A.G.,Liu, T.,Li, S.,Lin, H.L.,Zhang, Q.,Woods, V.L.,Stout, C.D.,Hollenberg, P.F.,Halpert, J.R.
Structural Analysis of Mammalian Cytochrome P450 2B4 Covalently Bound to the Mechanism-Based Inactivator tert-Butylphenylacetylene: Insight into Partial Enzymatic Activity.
Biochemistry, 50:4903-4911, 2011

PubMed Abstract: A combined structural and computational analysis of rabbit cytochrome P450 2B4 covalently bound to the mechanism-based inactivator tert-butylphenylacetylene (tBPA) has yielded insight into how the enzyme retains partial activity. Since conjugation to tBPA modifies a highly conserved active site residue, the residual activity of tBPA-labeled 2B4 observed in previous studies was puzzling. Here we describe the first crystal structures of a modified mammalian P450, which show an oxygenated metabolite of tBPA conjugated to Thr 302 of helix I. These results are consistent with previous studies that identified Thr 302 as the site of conjugation. In each structure, the core of 2B4 remains unchanged, but the arrangement of plastic regions differs. This results in one structure that is compact and closed. In this conformation, tBPA points toward helix B', making a 31° angle with the heme plane. This conformation is in agreement with previously performed in silico experiments. However, dimerization of 2B4 in the other structure, which is caused by movement of the B/C loop and helices F through G, alters the position of tBPA. In this case, tBPA lies almost parallel to the heme plane due to the presence of helix F' of the opposite monomer entering the active site to stabilize the dimer. However, docking experiments using this open form show that tBPA is able to rotate upward to give testosterone and 7-ethoxy-4-trifluoromethylcoumarin access to the heme, which could explain the previously observed partial activity.

PubMed: 21510666
DOI: 10.1021/bi200482g

Experimental method

X-RAY DIFFRACTION (3.5 Å)