Oxygen Activation and Radical Transfer in Ribonucleotide Reductase from Pathogens

病原体核糖核苷酸还原酶的氧活化和自由基转移

• 批准号: 8073451
• 负责人: JOSEPH M BOLLINGER
• 金额: $ 58.66万
• 依托单位: PENNSYLVANIA STATE UNIVERSITY, THE
• 依托单位国家: 美国
• 财政年份: 1997
• 资助国家: 美国
• 起止时间: 1997-01-01 至 2013-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8073451
• 关键词: Amino Acids; Antibiotics; Architecture; Aromatic Amino Acids; Binding; Biology; Catalysis; Chemicals; Chlamydia; Chlamydia trachomatis; Chlamydophila pneumoniae; Complex; Computing Methodologies; Coupled; Crystallography; Cysteine; DNA Repair; DNA biosynthesis; Deoxyribonucleotides; Development; Disease; Drug Delivery Systems; Electron Transport; Electrons; Enzymes; Escherichia coli; Event; Evolution; Free Radicals; Health; Holoenzymes; Homo sapiens; Human; Hydrogen; Hydroxylamine; Immune Targeting; Immune response; Iron; Kinetics; Manganese; Mediating; Metals; Mycobacterium tuberculosis; Natural regeneration; Nitrogen; Nucleotides; Organism; Oxidation-Reduction; Oxygen; Pathway interactions; Pharmaceutical Preparations; Phenylalanine; Positioning Attribute; Process; Proteins; Protons; Reaction; Reporting; Research; Resistance; Ribonucleotide Reductase; Ribonucleotide Reductase Inhibitor; Role; Simplexvirus; Site; Spectrum Analysis; Structure; System; Testing; Thermodynamics; Time; Tyrosine; Variant; Virus Diseases; abstracting; cancer therapy; carboxylate; cofactor; design; hydroxyurea; novel; nucleoside diphosphate; oxidation; pathogen; three dimensional structure

DESCRIPTION (provided by applicant): Ribonucleotide reductases (RNRs) provide deoxyribonucleotides for DNA synthesis and repair. The enzymes employ a conserved free-radical mechanism. Class I RNRs, including the human and Herpes Simplex Virus I enzymes, use a stable tyrosyl radical to initiate this mechanism and are validated drug targets. Several of the drugs function (at least in part) by reducing the tyrosyl radical. The tyrosyl radical is introduced into the enzyme by reaction of a di-iron(II) center with O2. Class I RNRs found in important human pathogens such as Chlamydia trachomatis and Mycobacterium tuberculosis lack the tyrosyl radical. The C. trachomatis RNR is, nevertheless, active. We recently showed that the C. trachomatis RNR uses a stable Mn(IV)/Fe(III) cofactor in place of the tyrosyl radical to initiates its reaction. The cofactor undergoes reduction to the Mn(III)/Fe(III) form to generate a protein radical that abstracts a hydrogen atom from the substrate. The Ct RNR is the first example of a manganese-dependent RNR, and its cofactor is the first example of a Mn/Fe redox center in biology. The cofactor is introduced, analogously to the tyrosyl radical in the conventional class I RNRs, by reaction of the reduced [Mn(II)/Fe(II)] metal center with O2. In this reaction, a Mn(IV)/Fe(IV) accumulates to a high level. In this project, we will elucidate the mechanisms of the formation and catalytic function of this novel cofactor. We will define the structures of its Mn(II)/Fe(II), Mn(IIII)/Fe(III), Mn(IV)/Fe(III) and Mn(IV)/Fe(IV) states by spectroscopic and computational methods and x-ray crystallography. We will understand how the protein protects the oxidized cofactor from adventitious reduction but then allows it to be reduced at the appropriate time to form the hydrogen-abstracting protein radical. We will study its chemical reactivity to uncover unique vulnerabilities that might be exploited in design of new drugs against the pathogens that use this type of RNR. Finally, we will compare the structures of closely related pairs of RNRs, of which one uses the standard tyrosyl radical and the other the novel Mn(IV)/Fe(III) cofactor, for clues to the design of both systems and the evolution of one from another. We will then attempt to use these clues to rationally convert one type of RNR into the other by changing crucial amino acids. PUBLIC HEALTH RELEVANCE: The enzyme ribonucleotide reductase (RNR) catalyzes the key step in DNA biosynthesis of all organisms and is a validated target for treatment of cancer and viral diseases. We recently reported that the class Ic RNR from the human pathogen Chlamydia trachomatis uses a novel redox cofactor (a heterobinuclear Mn/Fe cluster) to initiate catalysis. The structure and mechanism of this novel RNR will be elucidated to facilitate the rational development of class Ic RNR inhibitors that could be used to treat diseases caused by C. trachomatis and several other human pathogens (e.g. Chlamydia pneumoniae and Mycobacterium tuberculosis).

描述（由申请人提供）：核糖核苷酸还原酶（RNR）提供脱氧核糖核苷酸，用于DNA合成和修复。这些酶采用保守的自由基机制。 I类RNR，包括人类和单纯疱疹病毒I酶，使用稳定的酪酶自由基来启动这种机制并被经过验证的药物靶标。几种药物通过减少酪酶自由基的功能（至少部分）。酪酶自由基通过与O2的二铁（II）中心反应引入酶。在重要的人类病原体中发现的I类RNR，例如沙眼衣原体和结核分枝杆菌缺乏酪酶自由基。然而，沙眼C. c. rnr是活跃的。我们最近表明，沙眼C. rnr使用稳定的Mn（IV）/Fe（III）辅因子代替酪酶自由基来启动其反应。辅助因子还原为Mn（III）/Fe（III）形式，以产生一种从底物中抽象出氢原子的蛋白质自由基。 CT RNR是依赖锰的RNR的第一个例子，其辅助因子是生物学中MN/FE氧化还原中心的第一个例子。通过还原[Mn（ii）/Fe（ii）]金属中心的反应，在常规I rnR中类似地引入了辅因子，类似于常规I rnr中的酪酶自由基。在此反应中，MN（IV）/Fe（IV）积累到高水平。在这个项目中，我们将阐明这种新型辅助因子的形成和催化功能的机制。我们将通过光谱和计算方法和X射线晶体图定义其Mn（II）/Fe（II），MN（IIII）/FE（III），MN（IV）/FE（III）和Mn（IV）/Fe（IV）/Fe（IV）/Fe（IV）/Fe（iv）/Fe（iv）/Fe（iii）和X射线晶体学的结构。我们将了解蛋白质如何保护氧化的辅因子免受不定还原的降低，然后在适当的时间将其减少以形成氢吸收蛋白质自由基。我们将研究其化学反应性，以发现针对使用这种RNR的病原体设计新药时可能利用的独特漏洞。最后，我们将比较密切相关的RNR对的结构，其中一个使用标准的酪酶自由基，另一个使用新型MN（IV）/Fe（III）辅助因子，以了解系统的设计和一个从另一个系统的演变。然后，我们将尝试使用这些线索通过改变关键氨基酸来合理地将一种RNR转换为另一种RNR。公共卫生相关性：核糖核苷酸还原酶（RNR）催化所有生物体DNA生物合成的关键步骤，并且是治疗癌症和病毒疾病的验证靶标。我们最近报道说，来自人类病原体衣原体沙眼的IC RNR使用了一种新型的氧化还原辅助因子（杂核Mn/Fe簇）来启动催化。该新型RNR的结构和机制将被阐明，以促进可用于治疗由沙眼梭状芽孢杆菌和其他几种人类病原体引起的疾病的合理发展（例如，肺炎衣原体和结核分枝杆菌）。

项目成果

A long-lived, substrate-hydroxylating peroxodiiron(III/III) intermediate in the amine oxygenase, AurF, from Streptomyces thioluteus.

• DOI: 10.1021/ja9064969
• 发表时间: 2009-09-30
• 期刊: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
• 影响因子: 15
• 作者: Korboukh, Victoria Korneeva;Li, Ning;Barr, Eric W.;Bollinger, J. Martin, Jr.;Krebs, Carsten
• 通讯作者: Krebs, Carsten

Cyanobacterial alkane biosynthesis further expands the catalytic repertoire of the ferritin-like 'di-iron-carboxylate' proteins.

• DOI: 10.1016/j.cbpa.2011.02.019
• 发表时间: 2011-04
• 期刊: CURRENT OPINION IN CHEMICAL BIOLOGY
• 影响因子: 7.8
• 作者: Krebs, Carsten;Bollinger, J. Martin, Jr.;Booker, Squire J.
• 通讯作者: Booker, Squire J.

Structural basis for assembly of the Mn(IV)/Fe(III) cofactor in the class Ic ribonucleotide reductase from Chlamydia trachomatis.

• DOI: 10.1021/bi400819x
• 发表时间: 2013-09-17
• 期刊: BIOCHEMISTRY
• 影响因子: 2.9
• 作者: Dassama, Laura M. K.;Krebs, Carsten;Bollinger, J. Martin, Jr.;Rosenzweig, Amy C.;Boal, Amie K.
• 通讯作者: Boal, Amie K.

Formation and function of the Manganese(IV)/Iron(III) cofactor in Chlamydia trachomatis ribonucleotide reductase.

• DOI: 10.1021/bi8017625
• 发表时间: 2008-12-30
• 期刊: BIOCHEMISTRY
• 影响因子: 2.9
• 作者: Jiang, Wei;Yun, Danny;Saleh, Lana;Bollinger, J. Martin, Jr.;Krebs, Carsten
• 通讯作者: Krebs, Carsten

Substrate-triggered addition of dioxygen to the diferrous cofactor of aldehyde-deformylating oxygenase to form a diferric-peroxide intermediate.

• DOI: 10.1021/ja405047b
• 发表时间: 2013-10-23
• 期刊: Journal of the American Chemical Society
• 影响因子: 15
• 作者: Pandelia ME;Li N;Nørgaard H;Warui DM;Rajakovich LJ;Chang WC;Booker SJ;Krebs C;Bollinger JM Jr
• 通讯作者: Bollinger JM Jr