Metal ions in biological catalysis: from enzyme databases to general principles
Metal ions in biological catalysis: from enzyme databases to general principles
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DOI：
10.1007/s00775-008-0404-5
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发表时间：
2008-11-01
影响因子：
3
通讯作者：
Thornton, Janet M.
中科院分区：
文献类型：
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作者：
Andreini, Claudia;Bertini, Ivano;Thornton, Janet M.
我们使用现有的公共数据库和我们的新资源Metal-MACiE（http：//www.metal-MACiE）分析了金属离子在酶催化中的作用和分布。ebi AC. uk/thornton-srv/databases/Metal_MACiE/home.html）。在Metal-MACiE中，一个基于金属的反应机制的数据库，116个条目涵盖了21%的金属依赖性酶和70%的酶催化化学转化类型，根据金属功能进行了注释。我们使用Metal-MACiE来评估金属在生物催化中的功能，以及不同角色中不同金属的相对频率，这可能与它们各自的化学性质和环境中的可用性有关。从Metal-MACiE的概述中出现的总体情况是，氧化还原惰性金属离子在酶中用于稳定负电荷并凭借其刘易斯酸性质活化底物，而氧化还原活性金属离子既可用作刘易斯酸又可用作氧化还原中心。镁和锌是迄今为止最常见的第一种离子，而钙的使用相对较少。然而，镁最常与底物的磷酸基团结合，并且仅与酶瞬时相互作用，而其他金属稳定地与酶结合。第二类最常见的金属是铁，它在氧化还原反应的催化中占主导地位，其次是锰，钴，钼，铜和镍。氧化还原活性金属离子的反应性的控制可能涉及它们与有机辅因子的缔合以形成稳定单元。这种情况有时会发生在铁和镍上，而钴和钼则经常发生。
We analysed the roles and distribution of metal ions in enzymatic catalysis using available public databases and our new resource Metal-MACiE (http://www. ebi. ac. uk/thornton-srv/databases/Metal_MACiE/home.html). In Metal-MACiE, a database of metal-based reaction mechanisms, 116 entries covering 21% of the metal-dependent enzymes and 70% of the types of enzyme-catalysed chemical transformations are annotated according to metal function. We used Metal-MACiE to assess the functions performed by metals in biological catalysis and the relative frequencies of different metals in different roles, which can be related to their individual chemical properties and availability in the environment. The overall picture emerging from the overview of Metal-MACiE is that redox-inert metal ions are used in enzymes to stabilize negative charges and to activate substrates by virtue of their Lewis acid properties, whereas redox-active metal ions can be used both as Lewis acids and as redox centres. Magnesium and zinc are by far the most common ions of the first type, while calcium is relatively less used. Magnesium, however, is most often bound to phosphate groups of substrates and interacts with the enzyme only transiently, whereas the other metals are stably bound to the enzyme. The most common metal of the second type is iron, which is prevalent in the catalysis of redox reactions, followed by manganese, cobalt, molybdenum, copper and nickel. The control of the reactivity of redox-active metal ions may involve their association with organic cofactors to form stable units. This occurs sometimes for iron and nickel, and quite often for cobalt and molybdenum.