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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：
8549194
负责人：
Nigel Gordon RICHARDS
金额：
$ 28.14万
依托单位：
INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS
依托单位国家：
美国
项目类别：
财政年份：
2012
资助国家：
美国
起止时间：
2012-07-01 至 2015-06-30
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/8549194
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 Coupled 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 Sodium Chloride Solutions Structure Testing Therapeutic Transition Elements Translational Research United States National Institutes of Health 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. PUBLIC HEALTH RELEVANCE: Enzymes that can catalyze the breakdown of oxalic acid have potential therapeutic application in the treatment of human diseases associated with the accumulation of this compound in the blood and/or urine, including the formation of kidney stones. Our research group has played a leading role in characterizing the structure and catalytic mechanism of oxalate decarboxylase (OxDC), an oxalate-metabolizing enzyme that is present in fungi and some bacteria. In addition to providing new insights into the molecular mechanism by which OxDC can catalyze cleavage of the chemically unreactive C-C bond in oxalate, this project will also provide detailed information on how (i) protein environment can modulate transition metal chemistry, and (ii) amino acid mutations can be used to evolve new enzyme activities. Experiments will also be undertaken to assess the feasibility of employing OxDC in future, long-term translational research studies aimed at developing novel therapies for the clinical treatment and/or prevention of oxalate-related disease.

描述（由申请人提供）：可催化草酸分解的酶在治疗与该化合物在血液和/或尿液中蓄积相关的人类病理状况中具有潜在的治疗应用。该提案概述了旨在了解草酸脱羧酶（OxDC）的基本生物化学和调节的综合实验和计算研究的继续，该酶催化草酸转化为二氧化碳和甲酸。这两种产品都是无毒的，因此OxDC在治疗尿石症和/或预防基于草酸钙的结石形成方面具有临床应用的潜力。此外，锰依赖性的化学机制所采用的酶在已知的化学几乎没有先例，因此它的阐明将增加知识的过渡金属如何可能参与质子耦合电子转移，以产生活性自由基中间体，允许切割的化学惰性的草酸C-C键。在我们的第一个具体的目标，OxDC催化脱羧的催化机制的建议将使用先进的计算方法，X射线晶体学，以及一系列定点OxDC突变体的动力学和光谱表征进行测试。更具体地说，我们将进行X射线晶体学研究，旨在获得详细的结构信息草酸盐如何结合在活性位点内，在酶中的催化活性位点的数量，以及当OxDC/草酸盐复合物在有氧条件下翻转时分子氧结合的模式。此外，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，酶的位点特异性突变体的动力学特性将被测量，以描绘它们在催化和/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，一个关键目标将是研究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OxDC中Mn（II）中心的固有化学反应性。因此，在植物草酸氧化酶（OxOx）和OxDC中观察到的Mn结合基序的相似性提出了一个问题，即Mn（II）如何通过相同的配体进行协调，但在两种酶中的每一种中催化相同底物的不同化学转化。系统的生物物理，同位素效应和计算的一系列的OxOx/OxDC嵌合体的研究将进行验证现有的假设有关的分子基础的观察，改变一个关键的活性位点环废除脱羧活性与随之而来的氧化功能的增益。最后，在第三个目标中，我们将研究OxDC在各种类型的含盐溶液中溶解人类基于酒石酸钙的肾结石的能力，以便为该酶在临床应用中的后续使用提供基础。公共卫生关系：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疾病（包括肾结石的形成）中具有潜在的治疗应用。我们的研究小组在表征草酸脱羧酶（OxDC）的结构和催化机制方面发挥了主导作用，OxDC是一种存在于真菌和一些细菌中的草酸盐代谢酶。除了对OxDC催化草酸盐中化学不反应的C-C键裂解的分子机制提供新的见解外，该项目还将提供有关（i）蛋白质环境如何调节过渡金属化学的详细信息，以及（ii）氨基酸突变可用于进化新的酶活性。还将进行实验，以评估在未来的长期转化研究中使用OxDC的可行性，旨在开发用于临床治疗和/或预防糖尿病相关疾病的新疗法。

项目成果

期刊论文数量（23）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Membrane inlet for mass spectrometric measurement of catalysis by enzymatic decarboxylases.

DOI：
10.1016/j.ab.2011.06.031
发表时间：
2011-11-01
期刊：
Analytical biochemistry
影响因子：
2.9
作者：
Moral ME;Tu C;Richards NG;Silverman DN
通讯作者：
Silverman DN

Nitric oxide reversibly inhibits Bacillus subtilis oxalate decarboxylase.

一氧化氮可逆地抑制枯草芽孢杆菌草酸脱羧酶。

DOI：
10.1039/c0cc04946h
发表时间：
2011
期刊：
Chemical communications (Cambridge, England)
影响因子：
0
作者：
Moral,MarioEG;Tu,Chingkuang;Imaram,Witcha;Angerhofer,Alexander;Silverman,DavidN;Richards,NigelGJ
通讯作者：
Richards,NigelGJ

Formation of Hexacoordinate Mn(III) in Bacillus subtilis Oxalate Decarboxylase Requires Catalytic Turnover.

枯草芽孢杆菌草酸脱羧酶中六配位 Mn(III) 的形成需要催化转化。

DOI：
10.1021/acs.biochem.5b01340
发表时间：
2016
期刊：
Biochemistry
影响因子：
2.9
作者：
Zhu,Wen;Wilcoxen,Jarett;Britt,RDavid;Richards,NigelGJ
通讯作者：
Richards,NigelGJ

Sampling long time scale protein motions: OSRW simulation of active site loop conformational free energies in formyl-CoA:oxalate CoA transferase.

长时间尺度蛋白质运动采样：甲酰辅酶 A：草酸辅酶 A 转移酶活性位点环构象自由能的 OSRW 模拟。

DOI：
10.1021/ja101446u
发表时间：
2010
期刊：
Journal of the American Chemical Society
影响因子：
15
作者：
Lee,Sangbae;Chen,Mengen;Yang,Wei;Richards,NigelGJ
通讯作者：
Richards,NigelGJ

A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.

一种促进草酸脱羧酶中质子耦合电子转移的结构元件。

DOI：
10.1021/bi300001q
发表时间：
2012
期刊：
Biochemistry
影响因子：
2.9
作者：
Saylor,BenjaminT;Reinhardt,LaurieA;Lu,Zhibing;Shukla,MithilaS;Nguyen,Linda;Cleland,WWallace;Angerhofer,Alexander;Allen,KarenN;Richards,NigelGJ
通讯作者：
Richards,NigelGJ