肺炎链球菌Ap_nA水解酶SapH和酵母Ap_4A磷酸化酶Apa2的结构酶学研究
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摘要
二腺苷多聚磷酸(diadenosine polyphosphate, ApnAs)是一种核苷酸衍生物,主要由氨酰tRNA合成酶催化合成,是蛋白质合成过程的副产物。它广泛存在于各种生物中,作为细胞内和细胞外的调控分子发挥着重要的生理功能。这种核苷酸的在体内的积累会对一些关键酶如腺苷酸激酶和蛋白激酶等的活性有抑制作用,因此,生物体内ApnA的降解途径对保持细胞内这类核苷酸的稳态是非常重要的。
从原核到真核生物都存在着特异性的酶催化ApnA的降解,但在不同的物种中有所差别。降解ApnA的酶主要分为以下几大类：Nudix (nucleoside diphosphate linked to x)超家族蛋白,H·IT(histidine triad)超家族蛋白以及金属磷酸二酯酶超家族蛋白(metallophosphodiesterase, MPP)。我们选取肺炎链球菌(Streptococcus pneumoniae)R6菌株的SapH/Spr1479以及酿酒酵母(Saccharomyces cerevisiae)Apa2为研究目标,其分别属于MPP超家族和HIT超家族蛋白,均具有降解ApnA的功能,认为在参与ApnA的代谢过程有重要作用。
SapH是肺炎链球菌R6菌株中的一个分子量为33kDa的功能未知的蛋白。我们通过X-射线晶体学的方法解析了其apo-form,以及结合无机磷酸和AMP的复合物结构,分辨率分别为1.90A,2.30A和2.20A。SapH的核心结构采用四层的α-β-β-α折叠模式,这与MPP超家族蛋白类似。我们通过原子吸收和X-射线反常散射的方法鉴定出其活性中心的双金属为Fe3+和Mn2+,并且其与周围配位的残基形成正八面体的构象。酶活实验显示SapH除了具有典型的磷酸二酯酶的通用底物bis-(p-nitrophenyl) phosphate的水解活性外,还具有水解ApnA以及ATP的活性。突变试验表明金属配位的残基对于以上两种活性都是必须的。然而在复合物的结构中结合磷酸的Trp67仅在链球菌中保守,而且仅对ApnA和ATP的水解活性是不可或缺的。同时序列分析表明AMP的结合残基仅在链球菌中是保守的,因此(?)SapH是链球菌特有的一个双功能酶。
酿酒酵母降解Ap4A主要由两个同源性60%的Ap4A磷酸化酶(Apal和Apa2)完成。Apal和Apa2能可逆地催化Ap4A磷酸解为ATP和ADP,单独缺失apal, apa2以及双缺失apal和apa2虽然对酿酒酵母的生长没有太大影响,但都会导致细胞内的Ap4A浓度升高。我们通过X-射线晶体学的方法解析了Apa2的结构以及H161A突变体与Ap4A复合物的结构,分辨率分别为2.3A和(?)2.6A. Apa2采用a/p折叠模式,核心的β-sheet类似HIT超家族中的GalT(galactose-1-phosphate uridylyltransferase)家族蛋白,然而额外的亚结构域在Apa2中是特有的,同时也参与形成Ap4A的结合口袋。Ap4A的结合口袋可以分为AMP和ATP两个部分,二者在α-磷酸基团处以互相垂直的方式形成转角,进而将α-磷酸基团暴露给亲核攻击的催化残基His161,因此Apa2采用类似的GalT家族的双底物乒乓反应催化机制。活性检测显示Apal对Ap4A的相对活性仅为Apa2的1/7。其较低的活性主要是由于Apa2中稳定AMP部分的腺嘌呤的Phe68被Apal的Leu67取代。通过活性分析发现Apa2对Ap4A的活性最高,kcat/Km为21.0s-1μM-1。Apa2也具有磷酸解Ap3A和Ap5A的活性,但相对活性仅为Ap4A的1/12和1/3。由于Apa2的活性口袋能刚好容纳下Ap4A,所以Ap4A为其最适底物。序列比对表明Apa2在进化上代表了GalT家族的一个新的分支。我们不仅解析了HIT超家族中的第一个典型的Ap4A磷酸化酶的结构,而且是第一个HIT超家族中与Ap4A复合物的晶体结构。
Diadenosine polyphosphates (ApnAs) are a class of nucleotide derivatives distributed in all types of organisms. They are mainly produced by aminoacyl-tRNA synthetases as by-products during protein synthesis. They have emerged as intracellular and extracellular signal molecules implicated in the maintenance and regulation of vital cellular functions and become considered as second messengers. The accumulation of these molecules could inhibit the activity of several key enzymes such as adenylate kinases and protein kinases. Thus ApnAs metabolism, especially the degradation of these molecules is crucial for maintaining their intracellular homoestasis.
Specific enzymes for degrading ApnAs have been found in all kingdoms of life, and they could be generally classified into three categories, Nudix (nucleoside diphosphate linked to x) superfamily, HIT (histidine triad) superfamily and MPP (metallophosphodiesterase) superfamily. We selected Streptococcus pneumonia R6ApnA hydrolase Sprl479/SapH and Saccharomyces cerevisiae Ap4A phosphorylase Apa2as our targets. They belong to MPP and HIT superfamily, respectively, which are considered to be important for the homoestasis of ApnAs.
Sprl479from S. pneumoniae R6is a33-kDa hypothetical protein of unknown function. Here, we determined the crystal structures of its apo-form at1.90A, and complex forms with inorganic phosphate and AMP at2.30A and2.20A, respectively. The core structure of Sprl479adopts a four-layered α-β-β-α sandwich fold, with Fe3+and Mn2+coordinated at the binuclear center of the active site (similar to metallophosphoesterases). Enzymatic assays show that in addition to phosphodiesterase activity towards bis-(p-nitrophenyl) phosphate, Spr1479has hydrolase activity towards ApnA and ATP. Residues that coordinate with the two metals are indispensable for both activities. By contrast, the Strepttococci-specific residue Trp67, which binds to phosphate in the two complex structures, is indispensable for the ATP/ApnA hydrolase activity only. Moreover, the AMP-binding pocket is exclusively conserved in all Streptococci. Therefore, we named the protein SapH, for Streptococcal ATP/ApnA and phosphodiester hydrolase.
The degradation of Ap4A in S. cerevisiae is mainly catalyzed by two Ap4A phosphorylases (Apal and Apa2) with60%sequence identity. They could reversely catalyze the degradation of Ap4A into ADP and ATP. The disruption of apal alone, apa2alone, and both genes did not affect cell viability, whereas the absence of both genes could increase the intracellular concentration of Ap4A dramatically. Here we report the crystal structures of Apa2apo-form and Ap4A-complex form at2.3and2.6A, respectively. Apa2adopts an α/β fold, with the core structure of seven-stranded β-sheet resembling the GalT (galactose-1-phosphate uridylyltransferase) members of HIT superfamily. The additional sub-domain which is unique in Apa2forms a part of Ap4A-binding pocket. The AMP and ATP moiety of Ap4A is perpendicular to each other, thus exposing the a-phosphate group to the catalytic residue His161for nucleophilic attack. Similar to other GalT members, Apa2also adopts a ping-pong catalytic mechanism and forms the nucleotide-His intermediate. Enzymatic assays show that the relative activity of Apal towards Ap4A is only about one seventh of Apa2, which mainly results from the substitution of Leu67of Apal to Phe68of Apa2. In addition to Ap4A phosphorylase activity (kcat/Km of21.0s-1μM-1), Apa2also shows activity towards Ap3A and Ap5A, with the relative activity of one twelfth and one third to that of Ap4A, respectively. Ap4A is the favorable substrate because the binding pocket is perfectly complementary to a molecule of Ap4A. Multiple-sequence alignment reveals that Apa2evolves independently and represents a new branch of GalT family. This is also the first structure of a classic Ap4A phosphorylase in HIT superfamily.
从原核到真核生物都存在着特异性的酶催化ApnA的降解,但在不同的物种中有所差别。降解ApnA的酶主要分为以下几大类：Nudix (nucleoside diphosphate linked to x)超家族蛋白,H·IT(histidine triad)超家族蛋白以及金属磷酸二酯酶超家族蛋白(metallophosphodiesterase, MPP)。我们选取肺炎链球菌(Streptococcus pneumoniae)R6菌株的SapH/Spr1479以及酿酒酵母(Saccharomyces cerevisiae)Apa2为研究目标,其分别属于MPP超家族和HIT超家族蛋白,均具有降解ApnA的功能,认为在参与ApnA的代谢过程有重要作用。
SapH是肺炎链球菌R6菌株中的一个分子量为33kDa的功能未知的蛋白。我们通过X-射线晶体学的方法解析了其apo-form,以及结合无机磷酸和AMP的复合物结构,分辨率分别为1.90A,2.30A和2.20A。SapH的核心结构采用四层的α-β-β-α折叠模式,这与MPP超家族蛋白类似。我们通过原子吸收和X-射线反常散射的方法鉴定出其活性中心的双金属为Fe3+和Mn2+,并且其与周围配位的残基形成正八面体的构象。酶活实验显示SapH除了具有典型的磷酸二酯酶的通用底物bis-(p-nitrophenyl) phosphate的水解活性外,还具有水解ApnA以及ATP的活性。突变试验表明金属配位的残基对于以上两种活性都是必须的。然而在复合物的结构中结合磷酸的Trp67仅在链球菌中保守,而且仅对ApnA和ATP的水解活性是不可或缺的。同时序列分析表明AMP的结合残基仅在链球菌中是保守的,因此(?)SapH是链球菌特有的一个双功能酶。
酿酒酵母降解Ap4A主要由两个同源性60%的Ap4A磷酸化酶(Apal和Apa2)完成。Apal和Apa2能可逆地催化Ap4A磷酸解为ATP和ADP,单独缺失apal, apa2以及双缺失apal和apa2虽然对酿酒酵母的生长没有太大影响,但都会导致细胞内的Ap4A浓度升高。我们通过X-射线晶体学的方法解析了Apa2的结构以及H161A突变体与Ap4A复合物的结构,分辨率分别为2.3A和(?)2.6A. Apa2采用a/p折叠模式,核心的β-sheet类似HIT超家族中的GalT(galactose-1-phosphate uridylyltransferase)家族蛋白,然而额外的亚结构域在Apa2中是特有的,同时也参与形成Ap4A的结合口袋。Ap4A的结合口袋可以分为AMP和ATP两个部分,二者在α-磷酸基团处以互相垂直的方式形成转角,进而将α-磷酸基团暴露给亲核攻击的催化残基His161,因此Apa2采用类似的GalT家族的双底物乒乓反应催化机制。活性检测显示Apal对Ap4A的相对活性仅为Apa2的1/7。其较低的活性主要是由于Apa2中稳定AMP部分的腺嘌呤的Phe68被Apal的Leu67取代。通过活性分析发现Apa2对Ap4A的活性最高,kcat/Km为21.0s-1μM-1。Apa2也具有磷酸解Ap3A和Ap5A的活性,但相对活性仅为Ap4A的1/12和1/3。由于Apa2的活性口袋能刚好容纳下Ap4A,所以Ap4A为其最适底物。序列比对表明Apa2在进化上代表了GalT家族的一个新的分支。我们不仅解析了HIT超家族中的第一个典型的Ap4A磷酸化酶的结构,而且是第一个HIT超家族中与Ap4A复合物的晶体结构。
Diadenosine polyphosphates (ApnAs) are a class of nucleotide derivatives distributed in all types of organisms. They are mainly produced by aminoacyl-tRNA synthetases as by-products during protein synthesis. They have emerged as intracellular and extracellular signal molecules implicated in the maintenance and regulation of vital cellular functions and become considered as second messengers. The accumulation of these molecules could inhibit the activity of several key enzymes such as adenylate kinases and protein kinases. Thus ApnAs metabolism, especially the degradation of these molecules is crucial for maintaining their intracellular homoestasis.
Specific enzymes for degrading ApnAs have been found in all kingdoms of life, and they could be generally classified into three categories, Nudix (nucleoside diphosphate linked to x) superfamily, HIT (histidine triad) superfamily and MPP (metallophosphodiesterase) superfamily. We selected Streptococcus pneumonia R6ApnA hydrolase Sprl479/SapH and Saccharomyces cerevisiae Ap4A phosphorylase Apa2as our targets. They belong to MPP and HIT superfamily, respectively, which are considered to be important for the homoestasis of ApnAs.
Sprl479from S. pneumoniae R6is a33-kDa hypothetical protein of unknown function. Here, we determined the crystal structures of its apo-form at1.90A, and complex forms with inorganic phosphate and AMP at2.30A and2.20A, respectively. The core structure of Sprl479adopts a four-layered α-β-β-α sandwich fold, with Fe3+and Mn2+coordinated at the binuclear center of the active site (similar to metallophosphoesterases). Enzymatic assays show that in addition to phosphodiesterase activity towards bis-(p-nitrophenyl) phosphate, Spr1479has hydrolase activity towards ApnA and ATP. Residues that coordinate with the two metals are indispensable for both activities. By contrast, the Strepttococci-specific residue Trp67, which binds to phosphate in the two complex structures, is indispensable for the ATP/ApnA hydrolase activity only. Moreover, the AMP-binding pocket is exclusively conserved in all Streptococci. Therefore, we named the protein SapH, for Streptococcal ATP/ApnA and phosphodiester hydrolase.
The degradation of Ap4A in S. cerevisiae is mainly catalyzed by two Ap4A phosphorylases (Apal and Apa2) with60%sequence identity. They could reversely catalyze the degradation of Ap4A into ADP and ATP. The disruption of apal alone, apa2alone, and both genes did not affect cell viability, whereas the absence of both genes could increase the intracellular concentration of Ap4A dramatically. Here we report the crystal structures of Apa2apo-form and Ap4A-complex form at2.3and2.6A, respectively. Apa2adopts an α/β fold, with the core structure of seven-stranded β-sheet resembling the GalT (galactose-1-phosphate uridylyltransferase) members of HIT superfamily. The additional sub-domain which is unique in Apa2forms a part of Ap4A-binding pocket. The AMP and ATP moiety of Ap4A is perpendicular to each other, thus exposing the a-phosphate group to the catalytic residue His161for nucleophilic attack. Similar to other GalT members, Apa2also adopts a ping-pong catalytic mechanism and forms the nucleotide-His intermediate. Enzymatic assays show that the relative activity of Apal towards Ap4A is only about one seventh of Apa2, which mainly results from the substitution of Leu67of Apal to Phe68of Apa2. In addition to Ap4A phosphorylase activity (kcat/Km of21.0s-1μM-1), Apa2also shows activity towards Ap3A and Ap5A, with the relative activity of one twelfth and one third to that of Ap4A, respectively. Ap4A is the favorable substrate because the binding pocket is perfectly complementary to a molecule of Ap4A. Multiple-sequence alignment reveals that Apa2evolves independently and represents a new branch of GalT family. This is also the first structure of a classic Ap4A phosphorylase in HIT superfamily.
引文
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