Bridging Project 1: Amidohydrolase (AH) Superfamily

桥接项目 1：酰胺水解酶 (AH) 超家族

• 批准号: 7980207
• 负责人: JOHN A GERLT
• 金额: $ 23.78万
• 依托单位: UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN
• 依托单位国家: 美国
• 财政年份: 2010
• 资助国家: 美国
• 起止时间: 2010-05-20 至 2015-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7980207
• 关键词: Active Sites; Amides; Amidohydrolases; Amino Acids; Aromatic Amines; Binding; Biological Assay; C-terminal; Carbamates; Carbon Dioxide; Collaborations; Complex; Deamination; Decarboxylation; Divalent Cations; Electrostatics; Elements; Enzymes; Esters; Genome; Hydration status; Hydrogen Bonding; Hydroxide Ion; Hydroxides; In Vitro; Ions; Libraries; Ligands; Metals; Microbiology; Molecular Conformation; Mononuclear; Perch; Phosphoric Triester Hydrolases; Production; Proteins; Reaction; Resolution; Scheme; Screening procedure; Site; Solvents; Structure; Texas; Urease; Variant; Virtual Library; Water; Work; adenosine deaminase; amino group; carboxylate; functional group; genome sequencing; in vivo; inhibitor/antagonist; member; phosphate ester; small molecule

The AH superfamily was identified in 1997 when Holm and Sander recognized the structural and mechanistic similarities within adenosine deaminase (ADA), phosphotriesterase (PTE), and urease (URE) [1]. The structurally characterized members of this superfamily fold as a distorted (p/a)8-barrel with an active site that is perched at the C-terminal end of the (J-barrel [2]. The active sites contain either a binuclear metal center or one of two possible mononuclear metal centers. The substrate recognition elements are formed by the conformations of the eight loops that connect the eight p/a-fragments. Most reactions catalyzed by the AH superfamily are hydrolytic but members have been that catalyze decarboxylation, isomerization, hydration, and retroaldol reactions. Members of the AH superfamily have been found in every sequenced genome; the current estimate is that the superfamily contains > 13,000 unique sequences. About 0.5% of the enzymes in the protein universe belong to the AH superfamily. Metal centers. The most common metal center within the AH superfamily is binuclear where the two metal ions (Mn2+, Fe2+, or Ni2+) are ligated to the protein through electrostatic interactions with six amino acid residues. The a-metal (Ma) is coordinated to two His residues at the end of B-strand 1 and an Asp at the end of B-strand 8; the B-metal (M(b)) is coordinated to two His residues at the ends of B-strands 5 and 6. The metal ions are bridged to one another by a carbamate functional group formed by post-translational addition of CO2 to the ¿-amino group of a Lys at the end of B-strand 4. The metals are also bridged by a hydroxide from solvent. Variations on this theme include a Glu (at the end of either P-strand 3 or 4) as the bridging ligand and the substitution of an Asp for one of the His residues at the end of P-strand 1. In the most common mononuclear metal center a single divalent cation is bound to the Ma-site. The divalent cation is coordinated to the two conserved His residues at the end of P-strand 1, the His at the end of P-strand 5, and the invariant Asp at the end of B-strand 8; a water molecule is coordinated to the metal ion and to the His at the end of B-strand 6 and the Asp at the end of p-strand 8. A different mononuclear metal center is located at the Mp-site where the divalent cation is coordinated to His residues from B-strands 5 and 6 and another highly variable residue that can be either Cys or Glu; the coordination scheme is completed by a water molecule that is also hydrogen bonded to the Asp at the end of P-strand 8. Reactions catalyzed. More than 13,000 unique sequences have been identified in the AH superfamily. The sequences have been segregated into 9 major groups by the Superfamily/Genome Core, broadly represented by 24 clusters of orthologous groups (COGs) by the NCBI. More than 40 different reactions have been characterized for members of the AH superfamily; the number of reactions that remain to be discovered likely exceeds 100. The majority of the known reactions are hydrolytic reactions with carboxylate esters and amides and phosphate esters as substrates. The hydrolytic reactions also include deamination of aromatic amines. In addition, members of the AH superfamily catalyze decarboxylation.

AH 超家族于 1997 年被确定，当时 Holm 和 Sander 认识到腺苷脱氨酶 (ADA)、磷酸三酯酶 (PTE) 和脲酶 (URE) 之间的结构和机制相似性 [1]。 该超家族的结构特征成员折叠为扭曲的 (p/a)8 桶，其活性位点位于 (J 桶的 C 末端 [2]。活性位点包含双核金属中心或两个可能的单核金属中心之一由连接八个 p/a 片段的八个环的构象形成。 AH 超家族具有水解性，但其成员可催化脱羧、异构化、水合和逆羟醛反应；目前估计该超家族包含约 0.5% 的独特序列。蛋白质宇宙中的酶属于 AH 超家族。 AH 超家族中最常见的金属中心是双核的，其中两个金属离子（Mn2+、Fe2+ 或 Ni2+）通过与六个氨基酸残基的静电相互作用连接到蛋白质上。 B 链 1 末端有两个 His 残基，末端有一个 Asp B 链 8 的 B 金属 (M(b)) 与 B 链 5 和 6 末端的两个 His 残基配位。金属离子通过后形成的氨基甲酸酯官能团相互桥接。将 CO2 平移添加到 ¿ B 链 4 末端赖氨酸的氨基。金属也通过溶剂中的氢氧化物桥接。该主题的变体包括 Glu（位于 P 链 3 或 4 末端）作为桥联配体。以及用 Asp 取代 P 链 1 末端的 His 残基之一。 在最常见的单核金属中心，单个二价阳离子与 Ma 位点结合。二价阳离子与 P 链 1 末端的两个保守 His 残基、P 链 5 末端的 His 残基配位。 B 链 8 末端的不变 Asp 与金属离子和 B 链 6 末端的 His 以及 p 链 8 末端的 Asp 配位。单核金属中心 位于 Mp 位点，其中二价阳离子与 B 链 5 和 6 的 His 残基以及另一个高度可变的残基（可以是 Cys 或 Glu）配位，配位方案由同样是氢键的水分子完成；至 P 链 8 末端的 Asp。 已在 AH 超家族中鉴定出 13,000 多个独特序列，这些序列已被超家族/基因组核心分为 9 个主要组，由 NCBI 的 24 个直系同源组 (COG) 广泛代表。 AH 超家族成员的不同反应已被表征； 发现的可能超过100。大多数已知的反应是以羧酸酯和酰胺以及磷酸酯为底物的水解反应。此外，AH超家族的成员催化脱羧。