Metalloenzyme structure, function and assembly

金属酶的结构、功能和组装

• 批准号: 10621553
• 负责人: CATHERINE L DRENNAN
• 金额: $ 41.03万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-05-01 至 2028-04-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10621553
• 关键词: Amaze; Anabolism; Antibiotic Resistance; Antibiotics; Antineoplastic Agents; Antiviral Agents; Architecture; Biochemistry; Biological Models; Biotechnology; Carbon; Carbon Dioxide; Chemicals; Chemistry; Complex; Cryoelectron Microscopy; Crystallography; DNA biosynthesis; Data; Deoxyribonucleotides; Electron Transport; Enzymes; Gases; Hand; Health; Heart; Human; Ions; Life; Medical; Metalloproteins; Metals; Methane; Methods; Molecular; Molecular Conformation; Nature; Organometallic Chemistry; Production; Protein Engineering; Proteins; Reaction; Resolution; Ribonucleotide Reductase; Ribonucleotides; Scaffolding Protein; Structure; System; Toxic Environmental Substances; X-Ray Crystallography; anti-cancer; carbon compound; climate change; combat; design; frontier; greenhouse gases; improved; insight; metalloenzyme; microbial; novel; remediation; sample fixation; scaffold

Abstract The combination of metal ions with proteins offers unique chemical reactivities that are at the heart of many of Nature’s most important and amazing chemical transformations. For example, metalloenzymes catalyze the reduction of ribonucleotides to deoxyribonucleotides, a rate-limiting step in DNA biosynthesis. They biosynthesize anticancer and antiviral compounds that have unusual scaffolds and catalyze the carbon-carbon bond forming reactions that afford life on CO2 and H2 gases. Our lab employs structural methods to interrogate how metalloenzymes are able to perform this incredible chemistry. We seek to understand how the architecture of metalloenzymes allows for radical species to be controlled – i.e. turned off, turned on and harnessed – to enable the reaction at hand. We also strive to understand how proteins are designed to enable long-range electron transfer without protein damage or radical loss. In this proposal, we describe structural studies of our metalloenzyme model systems, including class Ia (diiron-dependent) and class III (glycyl radical- dependent) ribonucleotide reductases that allow us to interrogate the molecular basis of radical-based chemistry. We also describe efforts to understand how protein scaffolds facilitate organometallic chemistry, especially in regard to microbial carbon dioxide fixation and methane production. These studies leverage both our expertise in working with O2-sensitive metalloenzymes and in cryogenic-electron microscopy (cryo-EM). Although we will continue to employ X-ray crystallography, cryo-EM is proving to be a game-changer for many of our metalloenzyme systems. In particular, the resolution revolution of cryo-EM provides us with the means to obtain long-awaited structures of both large (2000 kDa) and transient metalloprotein complexes and to determine structures of metalloenzymes in functionally-essential conformational states that were previously unattainable by crystallography. The results of our structural studies will enable structure-based design of novel antibiotics targeting, for example, microbial ribonucleotide reductases. These structural data will also guide efforts to exploit radical enzymes for the production of medically important compounds with unusual scaffolds. These data will additionally facilitate the application of metalloenzymes or their bioinspired inorganic counterparts in the production of high-value carbon compounds from the greenhouse gas CO2 and, ideally, improve our understanding of some of the more enigmatic aspects of metalloprotein biochemistry.

抽象的 金属离子与蛋白质的结合提供了独特的化学反应性，这是许多化学反应的核心 例如，金属酶催化自然界最重要和最令人惊奇的化学转化。 核糖核苷酸还原为脱氧核糖核苷酸，这是 DNA 生物合成的限速步骤。 生物合成具有不寻常支架并催化碳-碳的抗癌和抗病毒化合物 为二氧化碳和氢气提供生命的成键反应我们的实验室采用结构方法来研究。 我们试图了解金属酶如何能够进行这种令人难以置信的化学反应。 金属酶的结构允许控制自由基物质——即关闭、打开和 利用——以实现手头的反应我们还努力了解蛋白质是如何设计来实现的。 没有蛋白质损伤或自由基损失的长程电子转移在这个提案中，我们描述了结构。 我们的金属酶模型系统的研究，包括 Ia 类（二铁依赖性）和 III 类（甘氨酰自由基） 依赖的）核糖核苷酸还原酶，使我们能够探究基于自由基的分子基础 我们还描述了理解蛋白质支架如何促进有机金属化学的努力， 特别是在微生物二氧化碳固定和甲烷生产方面，这些研究同时利用了两者。 我们在 O2 敏感金属酶和低温电子显微镜 (cryo-EM) 方面拥有专业知识。 尽管我们将继续使用 X 射线晶体学，但事实证明冷冻电镜对许多人来说是一个游戏规则改变者 特别是，冷冻电镜的分辨率革命为我们提供了实现这一目标的方法。 获得期待已久的大型（2000 kDa）和瞬时金属蛋白复合物的结构，并 确定以前发现的处于功能必需构象状态的金属酶的结构 我们的结构研究结果将实现基于结构的设计。 例如，针对微生物核糖核苷酸还原酶的新型抗生素也将这些结构数据。 指导利用自由基酶来生产具有不寻常的医学重要化合物的努力 这些数据还将促进金属酶或其仿生无机材料的应用。 从温室气体二氧化碳生产高价值碳化合物的单位，理想情况下， 提高我们对金属蛋白生物化学一些更神秘的方面的理解。

项目成果

Starting a new chapter on class Ia ribonucleotide reductases.

• DOI: 10.1016/j.sbi.2022.102489
• 发表时间: 2022-10
• 期刊: Current opinion in structural biology
• 影响因子: 6.8
• 作者: T. Levitz;C. Drennan

Development of an in vitro method for activation of X-succinate synthases for fumarate hydroalkylation.

• DOI: 10.1016/j.isci.2023.106902
• 发表时间: 2023-06-16
• 期刊: ISCIENCE
• 影响因子: 5.8
• 作者: Andorfer, Mary C.;King-Roberts, Devin T.;Imrich, Christa N.;Brotheridge, Balyn G.;Drennan, Catherine L.
• 通讯作者: Drennan, Catherine L.

Structural and spectroscopic analyses of the sporulation killing factor biosynthetic enzyme SkfB, a bacterial AdoMet radical sactisynthase.

• DOI: 10.1074/jbc.ra118.005369
• 发表时间: 2018-11-09
• 期刊: The Journal of biological chemistry
• 作者: Grell TAJ;Kincannon WM;Bruender NA;Blaesi EJ;Krebs C;Bandarian V;Drennan CL
• 通讯作者: Drennan CL

The Atypical Cobalamin-Dependent S-Adenosyl-l-Methionine Nonradical Methylase TsrM and Its Radical Counterparts.

• DOI: 10.1021/jacs.1c12064
• 发表时间: 2022-04-06
• 期刊: Journal of the American Chemical Society
• 影响因子: 15
• 作者: Ulrich EC;Drennan CL
• 通讯作者: Drennan CL

Structural and biochemical investigations of a HEAT-repeat protein involved in the cytosolic iron-sulfur cluster assembly pathway.

• DOI: 10.1038/s42003-023-05579-3
• 发表时间: 2023-12-18
• 期刊: COMMUNICATIONS BIOLOGY
• 影响因子: 5.9
• 作者: Vasquez, Sheena;Marquez, Melissa D.;Brignole, Edward J.;Vo, Amanda;Kong, Sunnie;Park, Christopher;Perlstein, Deborah L.;Drennan, Catherine L.
• 通讯作者: Drennan, Catherine L.