Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides

Subedi, Pradeep; Do, Hackwon; Lee, Jun Hyuck; Oh, Tae-Jin

doi:10.3390/ijms232113317

Open AccessArticle

Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides

¹

Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan 31460, Korea

²

Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Korea

³

Department of Polar Sciences, University of Science and Technology, Incheon 21990, Korea

⁴

Genome-Based BioIT Convergence Institute, Asan 31460, Korea

⁵

Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan 31460, Korea

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Int. J. Mol. Sci. 2022, 23(21), 13317; https://doi.org/10.3390/ijms232113317

Submission received: 1 October 2022 / Revised: 28 October 2022 / Accepted: 30 October 2022 / Published: 1 November 2022

(This article belongs to the Section Biochemistry)

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Abstract

Cytochrome P450 enzymes (CYPs) are heme-containing enzymes that catalyze hydroxylation with a variety of biological molecules. Despite their diverse activity and substrates, the structures of CYPs are limited to a tertiary structure that is similar across all the enzymes. It has been presumed that CYPs overcome substrate selectivity with highly flexible loops and divergent sequences around the substrate entrance region. Here, we report the newly identified CYP101D5 from Sphingomonas echinoides. CYP101D5 catalyzes the hydroxylation of β-ionone and flavonoids, including naringenin and apigenin, and causes the dehydrogenation of α-ionone. A structural investigation and comparison with other CYP101 families indicated that spatial constraints at the substrate-recognition site originate from the B/C loop. Furthermore, charge distribution at the substrate binding site may be important for substrate selectivity and the preference for CYP101D5.

Keywords: α/β-ionone; crystal structure; cytochrome P450; X-ray crystallography

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MDPI and ACS Style

Subedi, P.; Do, H.; Lee, J.H.; Oh, T.-J. Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides. Int. J. Mol. Sci. 2022, 23, 13317. https://doi.org/10.3390/ijms232113317

AMA Style

Subedi P, Do H, Lee JH, Oh T-J. Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides. International Journal of Molecular Sciences. 2022; 23(21):13317. https://doi.org/10.3390/ijms232113317

Chicago/Turabian Style

Subedi, Pradeep, Hackwon Do, Jun Hyuck Lee, and Tae-Jin Oh. 2022. "Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides" International Journal of Molecular Sciences 23, no. 21: 13317. https://doi.org/10.3390/ijms232113317

APA Style

Subedi, P., Do, H., Lee, J. H., & Oh, T.-J. (2022). Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides. International Journal of Molecular Sciences, 23(21), 13317. https://doi.org/10.3390/ijms232113317

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Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides

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