Pyrethroid Carboxylesterase PytH from Sphingobium faniae JZ-2: Structure and Catalytic Mechanism
Pyrethroid Carboxylesterase PytH from Sphingobium faniae JZ-2: Structure and Catalytic Mechanism
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扇形鞘氨醇 JZ-2 拟除虫菊酯羧酸酯酶 PytH：结构和催化机制
DOI：
10.1128/aem.02971-19
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发表时间：
2020-04
影响因子：
4.4
通讯作者：
Wang Weiwu
中科院分区：
文献类型：
--
作者：
Xu Dongqing;Gao Yanyan;Sun Bo;Ran Tingting;Zeng Liangping;He Jianhua;He Jian;Wang Weiwu
拟除虫菊酯类农药广泛应用于农业和家庭，然而，这些农药的广泛使用也会引起严重的环境和健康问题。羧酸酯酶水解拟除虫菊酯是微生物降解拟除虫菊酯的主要途径，但羧酸酯酶的结构及其催化机理尚不清楚。Sphingobium faniae JZ-2的羧酸酯酶PytH能有效水解多种拟除虫菊酯类农药。在这项研究中解决了PytH的晶体结构。这表明PytH属于具有典型催化Ser-His-Asp三联体的α/β-水解酶折叠蛋白，尽管PytH与它们的序列同源性较低（约20%）。特殊的大疏水结合口袋使PytH能够结合更大的拟除虫菊酯家族底物。我们的结构揭示了底物选择性和PytH的未来应用，加深了我们对α/β-水解酶成员的理解。摘要从拟除虫菊酯降解菌Sphingobium faniae JZ-2中分离得到的羧酸酯酶PytH能快速水解氯菊酯、甲氰菊酯、氯氰菊酯、氰戊菊酯、溴氰菊酯、三氟氯氰菊酯和联苯菊酯等多种拟除虫菊酯的酯键。为了阐明PytH的催化机理，我们在这里报告的晶体结构与联苯菊酯（BIF）和苯甲基磺酰氟（PMSF）和两个PytH突变体。虽然PytH与已报道的α/β-水解酶折叠蛋白具有低的序列同一性，但具有Ser-His-Asp三联体（Ser 78、His 230和Asp 202）的典型三联体催化中心是存在的，并且对于水解酶活性至关重要。然而，在我们解决的结构中没有发现Ser 78和His 230之间的接触，这可能是由于我们确定的PytH结构处于其无活性或低活性形式的事实。PytH的结构由核心结构域和盖结构域组成;来自两个结构域的底物周围的一些疏水氨基酸残基形成比其同源结构更深和更宽的疏水口袋。这表明较大的疏水口袋使PytH适合其较大的底物结合;盖和核心结构域都参与底物结合，并且盖结构域诱导的核心结构域移动可能使活性中心与底物正确定位。重要性拟除虫菊酯类杀虫剂广泛应用于农业和家庭;然而，这些杀虫剂的广泛使用也会导致严重的环境和健康问题。羧酸酯酶水解拟除虫菊酯是微生物降解拟除虫菊酯的主要途径，但羧酸酯酶的结构及其催化机理尚不清楚。Sphingobium faniae JZ-2的羧酸酯酶PytH能有效水解多种拟除虫菊酯类农药。在这项研究中解决了PytH的晶体结构。这表明PytH属于具有典型催化Ser-His-Asp三联体的α/β-水解酶折叠蛋白，尽管PytH与它们的序列同源性较低（约20%）。特殊的大疏水结合口袋使PytH能够结合更大的拟除虫菊酯家族底物。我们的结构揭示了底物选择性和PytH的未来应用，加深了我们对α/β-水解酶成员的理解。
Pyrethroid pesticides are widely applied in agriculture and household; however, extensive use of these pesticides also causes serious environmental and health problems. The hydrolysis of pyrethroids by carboxylesterases is the major pathway of microbial degradation of pyrethroids, but the structure of carboxylesterases and its catalytic mechanism are still unknown. Carboxylesterase PytH from Sphingobium faniae JZ-2 could effectively hydrolyze a wide range of pyrethroid pesticides. The crystal structures of PytH are solved in this study. This showed that PytH belongs to the α/β-hydrolase fold proteins with typical catalytic Ser-His-Asp triad, though PytH has a low sequence identity (about 20%) with them. The special large hydrophobic binding pocket enabled PytH to bind bigger pyrethroid family substrates. Our structures shed light on the substrate selectivity and the future application of PytH and deepen our understanding of α/β-hydrolase members. ABSTRACT Carboxylesterase PytH, isolated from the pyrethroid-degrading bacterium Sphingobium faniae JZ-2, could rapidly hydrolyze the ester bond of a wide range of pyrethroid pesticides, including permethrin, fenpropathrin, cypermethrin, fenvalerate, deltamethrin, cyhalothrin, and bifenthrin. To elucidate the catalytic mechanism of PytH, we report here the crystal structures of PytH with bifenthrin (BIF) and phenylmethylsulfonyl fluoride (PMSF) and two PytH mutants. Though PytH shares low sequence identity with reported α/β-hydrolase fold proteins, the typical triad catalytic center with Ser-His-Asp triad (Ser78, His230, and Asp202) is present and vital for the hydrolase activity. However, no contact was found between Ser78 and His230 in the structures we solved, which may be due to the fact that the PytH structures we determined are in their inactive or low-activity forms. The structure of PytH is composed of a core domain and a lid domain; some hydrophobic amino acid residues surrounding the substrate from both domains form a deeper and wider hydrophobic pocket than its homologous structures. This indicates that the larger hydrophobic pocket makes PytH fit for its larger substrate binding; both lid and core domains are involved in substrate binding, and the lid domain-induced core domain movement may make the active center correctly positioned with substrates. IMPORTANCE Pyrethroid pesticides are widely applied in agriculture and household; however, extensive use of these pesticides also causes serious environmental and health problems. The hydrolysis of pyrethroids by carboxylesterases is the major pathway of microbial degradation of pyrethroids, but the structure of carboxylesterases and its catalytic mechanism are still unknown. Carboxylesterase PytH from Sphingobium faniae JZ-2 could effectively hydrolyze a wide range of pyrethroid pesticides. The crystal structures of PytH are solved in this study. This showed that PytH belongs to the α/β-hydrolase fold proteins with typical catalytic Ser-His-Asp triad, though PytH has a low sequence identity (about 20%) with them. The special large hydrophobic binding pocket enabled PytH to bind bigger pyrethroid family substrates. Our structures shed light on the substrate selectivity and the future application of PytH and deepen our understanding of α/β-hydrolase members.
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DOI：
10.1007/978-0-387-77030-7_5
发表时间：
2008
影响因子：
6
作者：
C. Wheelock;B. Phillips;B. Anderson;Jeffrey L. Miller;Mike J Miller;B. Hammock
通讯作者：
C. Wheelock;B. Phillips;B. Anderson;Jeffrey L. Miller;Mike J Miller;B. Hammock
DOI：
10.1107/s0907444905001307
发表时间：
2005-04-01
影响因子：
2.2
作者：
Panjikar, S;Parthasarathy, V;Tucker, PA
通讯作者：
Tucker, PA
影响因子：
4.4
作者：
Wang, Bao-zhan;Guo, Peng;Li, Shun-peng
通讯作者：
Li, Shun-peng
DOI：
10.1107/s0108767300008849
发表时间：
2000-11
期刊：
Acta crystallographica. Section A, Foundations of crystallography
影响因子：
--
作者：
M. Delarue
通讯作者：
M. Delarue
影响因子：
4.4
作者：
Bao-zhan Wang;Peng Guo;Bao-jian Hang;Lian-tai Li;Jian He;Shun-Peng Li
通讯作者：
Bao-zhan Wang;Peng Guo;Bao-jian Hang;Lian-tai Li;Jian He;Shun-Peng Li