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    Home > The research team of Professor Zhang Qi of Fudan University and French scientists have revealed a new kind of dehydrating enzyme mechanism

    The research team of Professor Zhang Qi of Fudan University and French scientists have revealed a new kind of dehydrating enzyme mechanism

    • Last Update: 2018-02-06
    • Source: Internet
    • Author: User
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    Introduction S-adenosylmethionine (SAM) free radical enzyme is a kind of very ancient enzyme, which exists in the nature extensively and participates in many important biochemical reactions, such as DNA repair, RNA and protein modification, cofactor synthesis and so on It has unique reactivity and important scientific research value This kind of enzyme contains the characteristic tetrafe-4s cluster, which is used to reduce Sam in the process of reaction and generate a highly active 5 ˊ deoxyadenosine (5 ˊ DA) free radical, thus leading to a variety of biotransformation reactions Recently, Professor Zhang Qi's research group of Fudan University and the French Institute of structural biology cooperated to study the mechanism of Sam dependent dehydratase aprd4 in detail Zhang Qi, professor and doctoral supervisor of the Department of chemistry, Fudan University Since May 2014, he has worked in Fudan Department of chemistry Research interests are focused on the discovery, biosynthesis and mechanism of action of new antibiotics Professor Zhang Qi has won many awards, such as the "youth Millennium Program" of the Organization Department of the CPC Central Committee, the chemical structure association award of the American Chemical Society, and the young chemical biologist award of the International Chemical Biology Society (ICBs) At present, he is the deputy editor in chief of frontier in chemistry and the special reviewer of many magazines such as science In the past three years, he has published more than 20 papers in nat.commun., PNAs, j.am Chem SOC., angelw Chem Int ed and other magazines, and his achievements have been specially reported by C & en and other media Cutting edge scientific research achievements: Professor Zhang Qi's research group of Fudan University and French scientists have jointly revealed a new dehydrating enzyme mechanism, Apramycin, which is an important aminoglycoside antibiotic in clinic In the early stage of the research group of Professor Zhang Qi of Fudan University and the research group of Professor Yu Yi of Wuhan University, the gene cluster of Apramycin biosynthesis was cloned Through gene knockout and biochemical experiments in vitro, it is confirmed that aprd4 is a new type of Sam free radical enzyme, which is responsible for catalyzing the dehydration of the precursor, paromamine C3 ˊ Aprd4 and reductase aprd3 work together to realize the transformation from paromamine to lividamine, and then complete the oxidation of C6 ˊ under the action of flavin protein aprq (Figure 1) Fig 1 Aprd4 is the only Sam dependent dehydratase in the pathway of Apramycin biosynthesis (J am Chem SOC 2016, 138, 6427) The 1,2-hydroxy dehydration catalyzed by aprd4 requires a high energy barrier and is a relatively difficult chemical reaction There are many hypotheses about its catalytic mechanism, but there is no experimental evidence Recently, Zhang Qi's research group and yvain Nicolet, the French Institute of structural biology, worked together to analyze the catalytic mechanism of aprd4 in detail The researchers confirmed that the dehydration of aprd4 did not depend on K +, Ca2 + and other metal ions by ICP-AES experiment, and excluded the 1,2-hydroxy rearrangement mechanism By analyzing the crystal structure of aprd4, the complex proton transfer network in the catalytic reaction center was revealed Further site directed mutagenesis experiments confirmed the importance of the key amino acids of the proton transfer network (Fig 2) Figure 2 Study on the catalytic dehydration mechanism of aprd4: (a) proton transfer chain induced by substrate in the active center of aprd4 (b) site directed mutation and in vitro reaction results of important amino acids in the active center of aprd4 (source: J am Chem SOC., 2018, Doi: 10.1021/jacs.7b10501) further through DFT calculation, the researchers found that the conformation of D-glucosamine in the crystal had some flexibility, and the transition from half chair type to boat type had a lower energy barrier (< 5 Kcal / mol), through detailed structure comparison with other Sam free radical enzymes, it is concluded that the variability of this conformation plays a key role in C3 ˊ hydroxyl leaving process (Fig 3) Figure 3 Conformational changes of free radical intermediates in the process of aprd4 catalysis: (a) Theoretical Conformation needed to release water molecules: Newman model on both sides between the p-orbital (blue) of C4 ′ free radical center and the C3 ′ - OH bond; Periplanar region in gray, clinal region in the rest; angle values on both sides of chair conformation and ship conformation and C3 ′ - O distance are marked in green and red respectively (b) Based on the above results, the researchers speculated on the reaction mechanism of aprd4 (Fig 4) After the substrate enters the enzyme catalytic site, the 5 '- Da free radical grabs C4' hydrogen from the substrate and transfers it through the proton network to deprotonate the tyrosine residue y216 close to O4 '; the deprotonated y216 generates the key ketyl free radical (3) by accepting O4' proton (2); the thermal disturbance causes the conformational change of D-glucosamine ring and promotes the p-orbital, the intermediate of C4 'free radical It overlaps with σ C3 ′ - O3 ′ The protonated E280 is the most proton donor, which leads to the removal of water molecules (4) The tyrosine residue y216 can be reduced as a reductant to form lividamine (5) oxidized by C4 ′ The tyrosine residue regenerates and enters the next reaction cycle The discovery of the catalytic reaction mechanism not only promotes the further understanding of free radical enzymology, but also lays an important theoretical foundation for the engineering transformation of aminoglycoside antibiotics Figure 4 Schematic diagram of aprd4 catalytic mechanism reasoning (source: J am Chem SOC., 2018, DOI: 10.1021 / JACS 7b1051) This research result was published in the annals of the American Chemical Society (J am Chem SOC., 2018, DOI: 10.1021 / JACS 7b1051) Postdoctoral Liu wanqiu of Fudan University and Patricia Amara of the French Institute of structural biology are the co authors Professor Zhang Qi's research group homepage: http:// Professor Zhang Qi's information link: http:// yvain Nicolet's research group homepage: http:// from now on, CBG information decided to rename "CBG people" channel to "people and research" channel 。 After the name change, we will continue to pay attention to and follow up the scientific research activities and achievements of researchers, and report them in a richer form Today, science and technology elements are increasingly valued in economic life, China has ushered in the "node of science and technology explosion" Behind the progress of science and technology is the work of countless scientists In the field of chemistry, in the context of the pursuit of innovation driven, international cooperation has been strengthened, the influence of Returned Scholars in the field of R & D has become increasingly prominent, and many excellent research groups have emerged in China For this reason, CBG information adopts the 1 + X reporting mechanism CBG information, chembeango app, chembeango official microblog, CBG wechat subscription number and other platforms jointly launch the column of "people and scientific research", approach the representative research groups in China, pay attention to their research, listen to their stories, record their demeanor, and explore their scientific research spirit
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