酵母线粒体β-酮酰-ACP还原酶的结构生物学研究
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摘要
脂肪酸是自然界中极为重要的一类疏水性分子,在细胞内扮演着多种多样的角色。细菌、植物和动物细胞内都拥有各自的脂肪酸合成体系,负责以乙酰辅酶A和丙二酰辅酶A作为原料的从头合成。有两种类型的合成酶系统,Ⅰ型脂肪酸合成酶存在于脊椎动物、酵母细胞质基质以及一些细菌中,该酶只含一条或者两条庞大的多个结构域的多功能肽链。Ⅱ型脂肪酸合成酶存在于植物和大多数细菌中,是由不同基因编码多种不同的酶参与整个合成反应。近年来,研究发现在酿酒酵母线粒体中存在着Ⅱ型脂肪酸合酶。而针对该条合成代谢中各个反应来说,共计有六种基因参与编码这些酶,分别是ACPI, CEM1, MCT1, HTD2, ETR1和OAR1。其中OAR1基因负责编码线粒体β-酮酰-ACP还原酶(YmtOAR1),研究表明删除酵母细胞中的该基因直接导致呼吸缺陷型表型及生长的抑制。此外,线粒体中的脂肪酸合成体系被证明与tRNA的加工过程息息相关。
YmtOAR1属十SDR (short-chain alcohol dehydrogenase)蛋白家族,与其他物种的同源蛋白(FabG)存在20%-30%的同源性。但不同的是,一级序列中的插入序列及C-末端的缺失,导致了整体结构并没有呈现经典的Rossmann折叠花样,在溶液中呈现独特的二聚体聚合状态。YmtOAR1以辅酶NADPH作为负氢供体,通过质子传递,催化底物还原。本论文的研究工作解析了2.6A分辨率的apo-YmtOAR1晶体结构以及两套含有辅酶NADPH复合物的晶体结构。结构分析表明,YmtOAR1与所有已报道的同源蛋白有着明显的结构差异;且这种差异也从一定角度阐明了聚集状态与同源蛋白不同的原因。同时,YmtOAR1在结合辅酶后的构象发生了较为显著的变化,并且两套含配体的复合物晶体结构显示NADPH的构象亦略有不同。三套晶体结构可以用来模拟辅酶进入酶活口袋的动态过程。此外,在结构分析的基础上,通过定点突变和酶活性检测,确定了辅酶识别的关键残基Arg14,该残基对于辅酶识别酶是极其重要的,该残基的突变直接导致酶活性的丧失和极大地降低了酶对辅因子的亲和力。对于YmtOAR1的结构解析无疑拓展了我们对SDR家族蛋白丰富性的进一步认识,同时对更深入理解酶促反应机制提供了结构基础。
真核生物的内膜系统极为发达,不但区分了各种生化反应所发生的场所,也提供了各种细胞器之间的物质交流模式一一囊泡运输。转运囊泡包裹货物分子在一些特殊蛋白的辅助下,与特定的靶膜融合,从而完成对货物分子的筛选和运输。在SNARE和Sorting Nexins这两种蛋白家族的协助下,囊泡经过出芽或融合,后经分拣和运输,抵达靶位点。
存在于酿酒酵母细胞高尔基体到晚期溶酶体分拣途径中的重要蛋白Mvpl,是一个较为特殊的Sorting Nexins蛋白。MVP1基因与VPS1基因存在一定的联系性,过量表达Mvp1蛋白可抑制VPS1的几个等位基因。关于Mvp1蛋白参与囊泡分拣过程的机制目前还未阐明。本项研究结晶了Mvp1蛋白部分片段(⊿N117-Mvp1),尝试解析晶体结构,但由于衍射分辨率较低,故相应的优化工作仍在进行之中。
Fatty acid is a kind of very important hydrophobic molecule which plays a variety of roles in the cell. Fatty acid synthetase (FAS), a complex enzyme system, is responsible for de novo fatty acid synthesis from acetyl CoA or malonyl CoA in nature. Two main types of this enzyme system are found in a variety of species. The type Ⅰ FAS system is distributed in vertebrates, yeast cytoplasmic matrix and some bacteria. It is a single, large multifunctional polypeptide that catalyzes reactions involved in the elongation of the fatty acid chain. For many bacteria and plants, the type Ⅱ FAS system plays a major role in this process as a series of separate enzymes. Subsequent studies on FAS in organelles have revealed that there exists a mitochondrial type Ⅱ FAS in Saccharomyces cerevisiae. Mitochondrial FAS generates octanoyl-ACP used for the synthesis of lipoyl moieties and is also linked to RNA processing in both yeast and mammals. Yeast contains six genes encoding components of mitochondrial type Ⅱ FAS:ACPI, CEM1, MCT1, HTD2, ETR1and OARI. The OARI gene is responsible for encoding mitochondrial beta-ketoacyl-ACP reductase (YmtOAR1) and recent studies suggest that deletion of OARI leads to a respiratory deficient phenotype and causes growth inhibition.
Sequence alignments have shown that YmtOAR1belongs to a short-chain alcohol dehydrogenase (SDR) family and is20%-30%identical to homologous enzymes. Unlike other SDR family members. YmtOAR1forms a homodimer in solution. The overall structure of YmtOAR1does not show a canonical Rossmann fold due to the inserted sequence and the deletion of C-terminal. During the enzymatic reaction, with a hydride transfer from coenzyme NADPH followed by proton donation from YmtOAR1, the substrate was reduced. Here, we present the crystal structure of the YmtOAR1alone in apo-form at2.60A and complexed with NADPH at2.10A resolution. The enzyme generates significant conformational changes upon NADPH binding to the active site. Moreover, two different cofactor-binding patterns are observed from two forms of complex crystals. The two forms of NADPH bound enzyme may mimic the dynamic process of cofactor recognition. In addition, we found that the mutation of Argl4to alanine causes a loss of enzymatic activity and greatly decreases cofactor affinity. Structural and biochemical studies enable us to further understand the3-oxoacyl-(acyl-carrier-protein) reductases (OARs) of FAS and also provide some implications for cofactor recognition.
Eukaryotic membrane system is very sophisticated, not only to separate the place where a variety of biochemical reactions involved in, but also to exchange the substances between the various organelles-vesicle trafficking. The vesicles envelop cargo molecules, with the assistance of some special proteins, for example, SNARE or Sorting Nexins family, and take part in membrane fusion or budding, thereby completing the sorting and transport of cargos.
Mvp1protein is responsible for the sorting pathway between Golgi apparatus and late lysosome in Saccharomyces cerevisiae. As a unique gene, MVP1, that exhibits genetic interaction with VPS1and is itself required for vacuolar protein sorting has been isolated. Overproduction of Mvplp will suppress several dominant alleles of VPS1. The sorting mechanism of Mvpl involved in the vesicle transport process has not yet been elucidated. In this study, We crystallized the fragment of Mvp1(⊿N117-Mvp1), which attempts to resolve the crystal structure. Unfortunately, the crystals showed weak diffraction and further optimization work is still ongoing.
YmtOAR1属十SDR (short-chain alcohol dehydrogenase)蛋白家族,与其他物种的同源蛋白(FabG)存在20%-30%的同源性。但不同的是,一级序列中的插入序列及C-末端的缺失,导致了整体结构并没有呈现经典的Rossmann折叠花样,在溶液中呈现独特的二聚体聚合状态。YmtOAR1以辅酶NADPH作为负氢供体,通过质子传递,催化底物还原。本论文的研究工作解析了2.6A分辨率的apo-YmtOAR1晶体结构以及两套含有辅酶NADPH复合物的晶体结构。结构分析表明,YmtOAR1与所有已报道的同源蛋白有着明显的结构差异;且这种差异也从一定角度阐明了聚集状态与同源蛋白不同的原因。同时,YmtOAR1在结合辅酶后的构象发生了较为显著的变化,并且两套含配体的复合物晶体结构显示NADPH的构象亦略有不同。三套晶体结构可以用来模拟辅酶进入酶活口袋的动态过程。此外,在结构分析的基础上,通过定点突变和酶活性检测,确定了辅酶识别的关键残基Arg14,该残基对于辅酶识别酶是极其重要的,该残基的突变直接导致酶活性的丧失和极大地降低了酶对辅因子的亲和力。对于YmtOAR1的结构解析无疑拓展了我们对SDR家族蛋白丰富性的进一步认识,同时对更深入理解酶促反应机制提供了结构基础。
真核生物的内膜系统极为发达,不但区分了各种生化反应所发生的场所,也提供了各种细胞器之间的物质交流模式一一囊泡运输。转运囊泡包裹货物分子在一些特殊蛋白的辅助下,与特定的靶膜融合,从而完成对货物分子的筛选和运输。在SNARE和Sorting Nexins这两种蛋白家族的协助下,囊泡经过出芽或融合,后经分拣和运输,抵达靶位点。
存在于酿酒酵母细胞高尔基体到晚期溶酶体分拣途径中的重要蛋白Mvpl,是一个较为特殊的Sorting Nexins蛋白。MVP1基因与VPS1基因存在一定的联系性,过量表达Mvp1蛋白可抑制VPS1的几个等位基因。关于Mvp1蛋白参与囊泡分拣过程的机制目前还未阐明。本项研究结晶了Mvp1蛋白部分片段(⊿N117-Mvp1),尝试解析晶体结构,但由于衍射分辨率较低,故相应的优化工作仍在进行之中。
Fatty acid is a kind of very important hydrophobic molecule which plays a variety of roles in the cell. Fatty acid synthetase (FAS), a complex enzyme system, is responsible for de novo fatty acid synthesis from acetyl CoA or malonyl CoA in nature. Two main types of this enzyme system are found in a variety of species. The type Ⅰ FAS system is distributed in vertebrates, yeast cytoplasmic matrix and some bacteria. It is a single, large multifunctional polypeptide that catalyzes reactions involved in the elongation of the fatty acid chain. For many bacteria and plants, the type Ⅱ FAS system plays a major role in this process as a series of separate enzymes. Subsequent studies on FAS in organelles have revealed that there exists a mitochondrial type Ⅱ FAS in Saccharomyces cerevisiae. Mitochondrial FAS generates octanoyl-ACP used for the synthesis of lipoyl moieties and is also linked to RNA processing in both yeast and mammals. Yeast contains six genes encoding components of mitochondrial type Ⅱ FAS:ACPI, CEM1, MCT1, HTD2, ETR1and OARI. The OARI gene is responsible for encoding mitochondrial beta-ketoacyl-ACP reductase (YmtOAR1) and recent studies suggest that deletion of OARI leads to a respiratory deficient phenotype and causes growth inhibition.
Sequence alignments have shown that YmtOAR1belongs to a short-chain alcohol dehydrogenase (SDR) family and is20%-30%identical to homologous enzymes. Unlike other SDR family members. YmtOAR1forms a homodimer in solution. The overall structure of YmtOAR1does not show a canonical Rossmann fold due to the inserted sequence and the deletion of C-terminal. During the enzymatic reaction, with a hydride transfer from coenzyme NADPH followed by proton donation from YmtOAR1, the substrate was reduced. Here, we present the crystal structure of the YmtOAR1alone in apo-form at2.60A and complexed with NADPH at2.10A resolution. The enzyme generates significant conformational changes upon NADPH binding to the active site. Moreover, two different cofactor-binding patterns are observed from two forms of complex crystals. The two forms of NADPH bound enzyme may mimic the dynamic process of cofactor recognition. In addition, we found that the mutation of Argl4to alanine causes a loss of enzymatic activity and greatly decreases cofactor affinity. Structural and biochemical studies enable us to further understand the3-oxoacyl-(acyl-carrier-protein) reductases (OARs) of FAS and also provide some implications for cofactor recognition.
Eukaryotic membrane system is very sophisticated, not only to separate the place where a variety of biochemical reactions involved in, but also to exchange the substances between the various organelles-vesicle trafficking. The vesicles envelop cargo molecules, with the assistance of some special proteins, for example, SNARE or Sorting Nexins family, and take part in membrane fusion or budding, thereby completing the sorting and transport of cargos.
Mvp1protein is responsible for the sorting pathway between Golgi apparatus and late lysosome in Saccharomyces cerevisiae. As a unique gene, MVP1, that exhibits genetic interaction with VPS1and is itself required for vacuolar protein sorting has been isolated. Overproduction of Mvplp will suppress several dominant alleles of VPS1. The sorting mechanism of Mvpl involved in the vesicle transport process has not yet been elucidated. In this study, We crystallized the fragment of Mvp1(⊿N117-Mvp1), which attempts to resolve the crystal structure. Unfortunately, the crystals showed weak diffraction and further optimization work is still ongoing.
引文
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