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Biochemical Studies of Oxalate Decarboxylase

草酸脱羧酶的生化研究

基本信息

批准号：
7886215
负责人：
Nigel Gordon RICHARDS
金额：
$ 36.14万
依托单位：
UNIVERSITY OF FLORIDA
依托单位国家：
美国
项目类别：
财政年份：
2003
资助国家：
美国
起止时间：
2003-04-01 至 2014-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/7886215
关键词：
Active Sites Aerobic Amino Acids Bacteria Binding Biochemical Biochemistry Biological Models Blood Calcium Oxalate Calculi Carbon Dioxide Catalysis Chemicals Chemistry Chimera organism Clinical Clinical Treatment Complex Computing Methodologies Decarboxylation Development Dioxygen Disease Electron Transport Environment Enzymes Evolution Formates Future Goals Human Isotopes Kidney Calculi Kinetics Knowledge Ligands Liquid substance Literature Manganese Measurement Measures Mediating Metals Molecular Mutation Oxalate decarboxylase Oxalates Oxalic Acids Oxidases Plants Play Prevention Process Property Proteins Protons Reaction Recombinants Regulation Research Roentgen Rays Role Series Side Site Site-Directed Mutagenesis Solutions Structure Testing Therapeutic Transition Elements Translational Research Urine Work X-Ray Crystallography base clinical application clinically relevant computer studies enzyme activity fungus human disease insight mutant novel oxalate oxidase oxidation prevent protein folding public health relevance research study urolithiasis

项目摘要

DESCRIPTION (provided by applicant): Enzymes that can catalyze the breakdown of oxalic acid have potential therapeutic application in the treatment of human pathological conditions associated with the accumulation of this compound in the blood and/or urine. This proposal outlines the continuation of integrated experimental and computational studies aimed at understanding the fundamental biochemistry and regulation of oxalate decarboxylase (OxDC), an enzyme that catalyzes the conversion of oxalate to carbon dioxide and formate. Both of these products are non-toxic and so OxDC has the potential for clinical use in treating urolithiasis and/or preventing the formation of calcium oxalate-based stones. Moreover, the manganese-dependent chemical mechanism employed by the enzyme has little precedent in known chemistry, and so its elucidation will add to knowledge concerning how the transition metal might participate in proton-coupled electron transfer to yield reactive radical intermediates that permit cleavage of the chemically inert C-C bond of oxalate. In our first specific aim, proposals for the catalytic mechanism of OxDC-catalyzed decarboxylation will be tested using advanced computational methods, X-ray crystallography, and the kinetic and spectroscopic characterization of a series of site-directed OxDC mutants. More specifically, we will pursue X-ray crystallographic studies aimed at obtaining detailed structural information on how oxalate is bound within the active site, the number of catalytically active sites in the enzyme, and the mode of dioxygen binding when the OxDC/oxalate complex is turning over under aerobic conditions. In addition, DFT and DFT/MM calculations will be carried out to assess whether hypothetical intermediates, and their associated transition states, are consistent with the kinetic properties of OxDC. Finally, the kinetic properties of site-specific mutants of the enzyme will be measured to delineate their functional roles in catalysis and/or active site dynamics. These findings will be correlated with predictions made on the basis of X-ray crystallography and computational studies, and a key goal will be to examine the extent to which Mn(III) and Mn(IV) mediate catalysis. The second specific aim will focus on understanding how the protein environment can modulate the intrinsic chemical reactivity of the Mn(II) center(s) in bacterial OxDC. Thus, the similarity of the Mn-binding motifs observed in plant oxalate oxidases (OxOx) and OxDC raises the question of how Mn(II) can be coordinated by identical ligands but catalyze different chemical transformations of the same substrate in each of the two enzymes. Systematic biophysical, isotope effect and computational studies of a series of OxOx/OxDC chimeras will be undertaken to validate existing hypotheses concerning the molecular basis for the observation that changes to a critical active site loop abolish decarboxylative activity with concomitant gain of oxidative function. Finally, in the third aim, we will investigate the ability of OxDC to dissolve human, calcium oxalate-based kidney stones in various types of salt-containing solutions so as to provide a basis for subsequent use of the enzyme in clinical applications.

描述（由申请人提供）：可以催化草酸分解的酶在治疗与该化合物在血液和/或尿液中积累相关的人类病理状况中具有潜在的治疗应用。该提案概述了继续进行的综合实验和计算研究，旨在了解草酸脱羧酶（OxDC）的基本生物化学和调控，OxDC是一种催化草酸转化为二氧化碳和甲酸的酶。这两种产品都是无毒的，因此OxDC在治疗尿石症和/或预防草酸钙基结石的形成方面具有临床应用潜力。此外，该酶所采用的锰依赖化学机制在已知化学中几乎没有先例，因此它的阐明将增加关于过渡金属如何参与质子耦合电子转移以产生活性自由基中间体的知识，这些中间体允许草酸盐的化学惰性C-C键的裂解。在我们的第一个具体目标中，我们将使用先进的计算方法、x射线晶体学以及一系列位点导向的OxDC突变体的动力学和光谱表征来测试OxDC催化脱羧的催化机制。更具体地说，我们将进行x射线晶体学研究，旨在获得草酸盐如何在活性位点结合的详细结构信息，酶中催化活性位点的数量，以及氧dc /草酸盐复合物在有氧条件下翻转时的双氧结合模式。此外，还将进行DFT和DFT/MM计算，以评估假设的中间体及其相关的过渡态是否与OxDC的动力学性质一致。最后，将测量该酶的位点特异性突变体的动力学特性，以描述它们在催化和/或活性位点动力学中的功能作用。这些发现将与基于x射线晶体学和计算研究的预测相关联，一个关键目标将是检查Mn（III）和Mn（IV）介导催化的程度。第二个具体目标将集中在了解蛋白质环境如何调节细菌氧化dc中Mn（II）中心的内在化学反应性。因此，在植物草酸氧化酶（OxOx）和OxDC中观察到的Mn结合基元的相似性提出了Mn（II）如何能够被相同的配体协调，但在两种酶中催化相同底物的不同化学转化的问题。将对一系列OxOx/OxDC嵌合体进行系统的生物物理、同位素效应和计算研究，以验证现有的关于观察到关键活性位点环的变化会破坏脱羧活性并伴随氧化功能的增加的分子基础的假设。最后，在第三个目标中，我们将研究OxDC在不同类型的含盐溶液中溶解人草酸钙基肾结石的能力，为该酶在临床应用中的后续使用提供依据。