Resolving the Hydride Transfer Pathway in Oxidative Conversion of Proline to Pyrrole
Resolving the Hydride Transfer Pathway in Oxidative Conversion of Proline to Pyrrole
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DOI：
10.1021/acs.biochem.1c00741
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发表时间：
2022-02-01
期刊：
影响因子：
2.9
通讯作者：
Gumbart, James C.
中科院分区：
文献类型：
--
作者：
Acharya, Atanu;Yi, Dongqi;Gumbart, James C.
硫代模板化吡咯是合成许多天然产物的主要中间体，其中吡咯与载体蛋白（CP）连接。吡咯的生物合成需要L-脯氨酸侧链的氧化。本文中，我们通过分子动力学模拟、量子力学/分子力学模拟和电子结构计算，使用最近报道的（Thapa，H. R.，等人Biochemistry 2019，58，918）II型非核糖体蛋白合成酶（NRPS）Bmp 3-Bmp 1（氧化酶-CP）复合物的结构。底物（L-脯氨酸）与Bmp 1（CP）相连，催化位点位于黄素依赖性氧化酶（Bmp 3）内部。我们表明，FAD isoalloxazine环稳定在Bmp 3的催化位点通过强氢键与Asn 123，Ile 12 S，Ser 126，和Thr 158。在初始去质子化之后，接着是烯胺-亚胺互变异构化，通过氢化物转移（从C3或N1）氧化C2-C3或C2-N1键对于吡咯合成是需要的。计算结果表明，氢化物转移更可能发生在C3比N1。此外，我们通过酶促合成脯氨酸衍生物证明了氧化酶活性位点的弹性。
Thiotemplated pyrrole is a prevailing intermediate in the synthesis of numerous natural products in which the pyrrole is tethered to a carrier protein (CP). Biosynthesis of the pyrrole requires oxidation of an L-proline side chain. Herein, we investigate the biocatalytic mechanism of proline-to-pyrrole synthesis by molecular dynamics simulations, quantum mechanics/molecular mechanics simulations, and electronic structure calculations using the recently reported (Thapa, H. R., et al. Biochemistry 2019, 58, 918) structure of a type II nonribosomal protein synthetase (NRPS) Bmp3-Bmp1 (Oxidase-CP) complex. The substrate (L-proline) is attached to the Bmp1 (CP), and the catalytic site is located inside the flavin-dependent oxidase (Bmp3). We show that the FAD isoalloxazine ring is stabilized in the catalytic site of Bmp3 by strong hydrogen bonding with Asn123, Ile12S, Ser126, and Thr158. After the initial deprotonation followed by an enamine-imine tautomerization, oxidation of the C2-C3 or C2-N1 bond, through a hydride transfer (from either C3 or N1), is required for the pyrrole synthesis. Computational results indicate that the hydride transfer is more likely to occur from C3 than N1. Additionally, we demonstrate the elasticity in the oxidase active site through enzymatic synthesis of proline derivatives.