Article pubs.acs.org/IC
Cite This: Inorg. Chem. XXXX, XXX, XXX−XXX
Oxidative Rearrangement Mechanism of Pentalenolactone F Catalyzed by Cytochrome P450 CYP161C2 (PntM) Xiya Wang,† Junyou Shi,‡ and Yongjun Liu*,† †
Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, People’s Republic of China ‡ College of Chemistry and Environmental Science, Qujing Normal University, Qujing, Yunnan 655011, People’s Republic of China
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S Supporting Information *
ABSTRACT: The CYP161C2 (PntM) from Streptomyces arenae is a member of the cytochrome P450 enzymes, which catalyzes the unusual oxidative rearrangement of pentalenolactone F (1) to the sesquiterpenoid antibiotic pentalenolactone (3). On the basis of the crystal structure of PntM bound with substrate, quantum mechanical/molecular mechanics (QM/MM) calculations have been performed to explore the detailed mechanism of PntMcatalyzed oxidative rearrangement. The conversion from pentalenolactone F (1) to pentalenolactone (3) involves the stereospecific removal of the H-1si from 1, the syn-1,2-migration of the 2si methyl group, and the antarafacial loss of H-3re. The abstraction of H-1si by Cpd I is calculated to be rate limiting with an energy barrier of 20.3 kcal/mol, which basically agrees with the estimated free energy barrier from experiments (18.6 kcal/mol). It is the unfavorable geometry of Fe−OH−C1 that blocks the oxygen rebound reaction, and the subsequent intramolecular syn-1,2-methyl migration is accompanied by an electron transfer from the substrate to the porphyrin ring via an Fe−OH group, generating the carbocation intermediate. Owing to the positive charge, the intermediate can easily lose a proton to form the final products. Our calculation results indicate that both the carboxyl group of porphyrin and Fe−OH can act as bases to accept the proton of the substrate. The target product pentalenolactone and the three isomeric byproducts correspond to four different modes of deprotonation.
1. INTRODUCTION
target glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase, making the pentalenolactone possess antibiotic activity.7−9 The PntM and PenM are orthologous enzymes which share 81% mutual sequence identity and 87% similarity, and both of them are composed of 398 amino acids.6 Several groups have conducted research to explore the catalytic mechanism of PntM.10−19 Early in the 1970s and 1980s, Cane et al.10,11 revealed the origin of pentalenolactone by growth of Streptomyces UC5319 in the media that contains [U-13C6] glucose. At present, the rearrangement of pentalenolactone F to pentalenolactone has biochemical precedent among all known CYP-catalyzed reactions. As in other P450catalyzed reactions,20−22 the oxoiron(IV) porphyrin cation radical intermediate (compound I) of PntM first abstracts a hydrogen atom (H-1si) to form the [FeIII-OH] species.12 However, in the common P450-catalyzed reactions, oxygen rebound often follows the hydrogen abstraction,23,24 and the rate constant for the usual oxygen rebound is >1010−1011 s−1. Thus, the oxygen rebound competes with rapid electron transfer to the [FeIII-OH] with a rate of
