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(申请人提供)：核糖核苷酸还原酶(RNR)为DNA合成和修复提供脱氧核糖核苷酸。这些酶采用一种保守的自由基机制。第一类RNRs，包括人类和单纯疱疹病毒I型酶，使用稳定的酪氨酸基启动这一机制，是有效的药物靶点。有几种药物的作用(至少部分)是通过减少酪氨酸基起作用的。酪氨酸基通过二铁(II)中心与O2反应引入酶中。在重要的人类病原体如沙眼衣原体和结核分枝杆菌中发现的I类RNRs缺乏酪氨酸基。然而，沙眼衣原体RNR是活跃的。我们最近发现沙眼衣原体RNR使用稳定的Mn(IV)/Fe(III)辅助因子来代替酪氨酸自由基来启动其反应。辅因子经历还原为Mn(III)/Fe(III)形式以生成蛋白质自由基，该蛋白质自由基从底物中提取氢原子。Ct RNR是第一个依赖于锰的RNR的例子，它的辅因子是生物学上第一个Mn/Fe氧化还原中心的例子。通过还原的[Mn(II)/Fe(II)]金属中心与O2反应，引入了类似于传统I类RNRs中的酪氨酸自由基的辅因子。在该反应中，Mn(IV)/Fe(IV)积累到很高的水平。在这个项目中，我们将阐明这种新型辅因子的形成和催化作用的机制。我们将用光谱学、计算方法和X-射线结晶学方法确定其Mn(II)/Fe(II)、Mn(III)/Fe(III)、Mn(IV)/Fe(III)和Mn(IV)/Fe(IV)的结构。我们将了解蛋白质如何保护被氧化的辅因子免受不定还原，但随后允许它在适当的时间被还原以形成吸氢蛋白质自由基。我们将研究它的化学反应能力，以揭示可能在设计针对使用这种类型的RNR的病原体的新药时利用的独特漏洞。最后，我们将比较紧密相关的RNRs对的结构，其中一对使用标准酪氨酸根，另一对使用新的Mn(IV)/Fe(III)辅因子，以寻找这两个系统的设计和一个系统的进化的线索。然后，我们将尝试利用这些线索，通过改变关键氨基酸来合理地将一种类型的RNR转换为另一种类型的RNR。与公共健康相关：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，是治疗癌症和病毒疾病的有效靶点。我们最近报道了来自人类病原体沙眼衣原体的类IC RNR使用一种新的氧化还原辅助因子(异双核Mn/Fe簇)来启动催化。这种新型RNR的结构和机制将被阐明，以促进IC类RNR抑制剂的合理开发，这些抑制剂可用于治疗沙眼衣原体和其他几种人类病原体(如肺炎衣原体和结核分枝杆菌)引起的疾病。

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.

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

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