Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways
Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways
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DOI：
10.1021/ci700006f
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发表时间：
2007-07-01
影响因子：
5.6
通讯作者：
Kanehisa, Minoru
中科院分区：
文献类型：
--
作者：
Oh, Mina;Yamada, Takuji;Kanehisa, Minoru
化合物在生物系统中的作用现在通过高通量实验技术系统地分析。为了自动处理和解释大规模数据，有必要开发生物信息学方法，通过考虑涉及蛋白质和其他生物大分子的相互作用和反应，从这些小分子的化学结构中提取信息。在这里，我们专注于代谢化合物，并提出了一个知识为基础的方法来了解反应性和代谢的命运在酶催化的反应在一个给定的有机体或组。我们首先构建了KEGG RPAIR数据库，其中包含5734个已知酶催化反应中的7091个反应物对（底物-产物对）的化学结构对齐和结构转换模式（称为RDM模式）。然后根据KEGG PATHWAY数据库对总共2205个RDM模式进行分类。大多数RDM模式是唯一的或优先发现在特定类别的途径，虽然一些RDM模式，如涉及磷酸化，是普遍存在的。外源性物质的生物降解途径包含最不同的RDM模式，我们开发了一个计划，用于预测细菌的生物降解途径，例如，环境化合物的化学结构。
The roles of chemical compounds in biological systems are now systematically analyzed by high-throughput experimental technologies. To automate the processing and interpretation of large-scale data it is necessary to develop bioinformatics methods to extract information from the chemical structures of these small molecules by considering the interactions and reactions involving proteins and other biological macromolecules. Here we focus on metabolic compounds and present a knowledge-based approach for understanding reactivity and metabolic fate in enzyme-catalyzed reactions in a given organism or group. We first constructed the KEGG RPAIR database containing chemical structure alignments and structure transformation patterns, called RDM patterns, for 7091 reactant pairs (substrate-product pairs) in 5734 known enzyme-catalyzed reactions. A total of 2205 RDM patterns were then categorized based on the KEGG PATHWAY database. The majority of RDM patterns were uniquely or preferentially found in specific classes of pathways, although some RDM patterns, such as those involving phosphorylation, were ubiquitous. The xenobiotics biodegradation pathways contained the most distinct RDM patterns, and we developed a scheme for predicting bacterial biodegradation pathways given chemical structures of, for example, environmental compounds.