Functional annotation of haloacid dehalogenase superfamily structural genomics proteins
Functional annotation of haloacid dehalogenase superfamily structural genomics proteins
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DOI：
10.1042/bcj20230057
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发表时间：
2023-10-01
影响因子：
4.1
通讯作者：
Ondrechen，Mary Jo
中科院分区：
文献类型：
--
作者：
Kankanamge，Lakindu S. Pathira;Ruffner，Lydia A.;Ondrechen，Mary Jo
卤酸脱卤酶（HAD）是一个大的超家族的成员，该家族包括许多功能性不佳的结构基因组蛋白。该超家族由多种类型的酶组成，这些酶可以充当糖磷酸酶、卤酸脱卤酶、膦酰基乙醛水解酶、ATP酶或磷酸单酯酶。在这里，我们报告预测的功能注释和实验测试的直接生化分析的结构基因组蛋白从HAD超家族。为了表征HAD超家族成员的功能，分析了9个代表性的HAD蛋白和21个结构基因组蛋白。使用技术的基础上计算的化学和静电特性的个别氨基酸，从HAD超家族的5个结构基因组蛋白的功能进行预测和验证的生化测定。脱卤酶样水解酶RSc 1362（Uniprot Q8 XZN 3，PDB 3UMB）被预测为脱卤酶，并且脱卤酶活性被实验证实。四种蛋白质被预测为糖磷酸酶，其特征如下：（Uniprot Q978 Y 6）具有海藻糖-6-磷酸磷酸酶和果糖-6-磷酸酶活性;来自多形拟杆菌的卤酸脱卤酶样水解酶（Uniprot Q8 A2 F3; PDB 3 NIW），具有果糖-6-磷酸磷酸酶和蔗糖-6-磷酸酶活性;来自直肠真杆菌的假定磷酸酶（Uniprot D 0 VWU 2; PDB 3DAO）作为蔗糖-6-磷酸磷酸酶;和来自嗜热土芽孢杆菌的假定蛋白质（Uniprot Q5 L139; PDB 2 PQ 0）作为果糖-6-磷酸酶。大多数这些糖磷酸酶表现出一定的底物混杂。
Haloacid dehalogenases (HAD) are members of a large superfamily that includes many Structural Genomics proteins with poorly characterized functionality. This superfamily consists of multiple types of enzymes that can act as sugar phosphatases, haloacid dehalogenases, phosphonoacetaldehyde hydrolases, ATPases, or phosphate monoesterases. Here, we report on predicted functional annotations and experimental testing by direct biochemical assay for Structural Genomics proteins from the HAD superfamily. To characterize the functions of HAD superfamily members, nine representative HAD proteins and 21 structural genomics proteins are analyzed. Using techniques based on computed chemical and electrostatic properties of individual amino acids, the functions of five structural genomics proteins from the HAD superfamily are predicted and validated by biochemical assays. A dehalogenase-like hydrolase, RSc1362 (Uniprot Q8XZN3, PDB 3UMB) is predicted to be a dehalogenase and dehalogenase activity is confirmed experimentally. Four proteins predicted to be sugar phosphatases are characterized as follows: a sugar phosphatase fromThermophilus volcanium(Uniprot Q978Y6) with trehalose-6-phosphate phosphatase and fructose-6-phosphate phosphatase activity; haloacid dehalogenase-like hydrolase fromBacteroides thetaiotaomicron(Uniprot Q8A2F3; PDB 3NIW) with fructose-6-phosphate phosphatase and sucrose-6-phosphate phosphatase activity; putative phosphatase fromEubacterium rectale(Uniprot D0VWU2; PDB 3DAO) as a sucrose-6-phosphate phosphatase; and hypothetical protein fromGeobacillus kaustophilus(Uniprot Q5L139; PDB 2PQ0) as a fructose-6-phosphate phosphatase. Most of these sugar phosphatases showed some substrate promiscuity.