7E7F

Human CYP11B1 mutant in complex with metyrapone

Summary for 7E7F

• Entry DOI: 10.2210/pdb7e7f/pdb
• Descriptor: Cytochrome P450 11B1, mitochondrial, PROTOPORPHYRIN IX CONTAINING FE, METYRAPONE, ... (6 entities in total)
• Functional Keywords: p450, oxidoreductase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 57665.43

Authors

Mukai, K.,Sugimoto, H.,Reiko, S.,Matsuura, T.,Hishiki, T.,Kagawa, N. (deposition date: 2021-02-26, release date: 2022-01-05, Last modification date: 2023-11-29)

Primary citation

Mukai, K.,Sugimoto, H.,Kamiya, K.,Suzuki, R.,Matsuura, T.,Hishiki, T.,Shimada, H.,Shiro, Y.,Suematsu, M.,Kagawa, N.
Spatially restricted substrate-binding site of cortisol-synthesizing CYP11B1 limits multiple hydroxylations and hinders aldosterone synthesis.
Curr Res Struct Biol, 3:192-205, 2021

PubMed Abstract: Human cytochromes P450 (CYP11B1) and P450 (CYP11B2) are monooxygenases that synthesize cortisol through steroid 11β-hydroxylation and aldosterone through a three-step process comprising 11β-hydroxylation and two 18-hydroxylations, respectively. CYP11B1 also catalyzes 18-monohydroxylation and 11β,18-dihydroxylation. To study the molecular basis of such catalytic divergence of the two enzymes, we examined a CYP11B1 mutant (Mt-CYP11B1) with amino acid replacements on the distal surface by determining the catalytic activities and crystal structure in the metyrapone-bound form at 1.4-Å resolution. Mt-CY11B1 retained both 11β-hydroxylase and 18-hydroxylase activities of the wild type (Wt-CYP11B1) but lacked 11β,18-dihydroxylase activity. Comparisons of the crystal structure of Mt-CYP11B1 to those of Wt-CYP11B1 and CYP11B2 that were already reported show that the mutation reduced the innermost space putatively surrounding the C3 side of substrate 11-deoxycorticosterone (DOC) bound to Wt-CYP11B1, while the corresponding space in CYP11B2 is enlarged markedly and accessible to bulk water through a channel. Molecular dynamics simulations of their DOC-bound forms supported the above findings and revealed that the enlarged space of CYP11B2 had a hydrogen bonding network involving water molecules that position DOC. Thus, upon positioning 11β-hydroxysteroid for 18-hydroxylation in their substrate-binding sites, steric hindrance could occur more strongly in Mt-CYP11B1 than in Wt-CYP11B1 but less in CYP11B2. Our investigation employing Mt-CYP11B1 sheds light on the divergence in structure and function between CYP11B1 and CYP11B2 and suggests that CYP11B1 with spatially-restricted substrate-binding site serves as 11β-hydroxylase, while CYP11B2 with spatially-extended substrate-binding site successively processes additional 18-hydroxylations to produce aldosterone.

PubMed: 34485929
DOI: 10.1016/j.crstbi.2021.08.001

Experimental method

X-RAY DIFFRACTION (1.4 Å)