Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases.
Distribution and prediction of catalytic domains in 2-oxoglutarate dependent dioxygenases.
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DOI：
10.1186/1756-0500-5-410
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发表时间：
2012-08-04
影响因子：
1.8
通讯作者：
Kundu S
中科院分区：
文献类型：
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作者：
Kundu S
2-酮戊二酸依赖性超家族是一组多样的非血红素双加氧酶，并且存在于原核生物、真核生物和古细菌中。不同的酶在底物的偏好和反应化学，一个因素，排除了它们的分类，仅通过同源性研究和电子注释计划。在这项工作中，我建议和探索的基本原理，使用基板分类结构相似的α-酮戊二酸依赖酶。2-OG依赖性酶的系统发育分支中的差异催化由活性位点氨基酸的子集的相互作用决定。用现有的计算方法识别这些蛋白质是具有挑战性的，并且对所有蛋白质都不可行。一个聚类协议的基础上验证机制的已知分子的催化，在串联组特定的隐马尔可夫模型配置文件是能够区分和隔离这些酶。通过网络服务器访问该储存库，该网络服务器将用户定义的未知序列与这些预定义的概况进行比较，并输出预测的催化结构域的列表。该服务器是免费的，可通过以下URL访问（http：//comp-biol.theacms.in/H2OGpred.html）。提出的分层是一种新的尝试，在分类和预测2-酮戊二酸依赖性功能。此外，该服务器将为研究人员提供一个工具，将他们的数据与催化域的HMM配置文件的综合列表进行比较。这项工作将有助于研究人员筛选和表征推定的2-OG依赖性序列。简介数据库将定期更新。
The 2-oxoglutarate dependent superfamily is a diverse group of non-haem dioxygenases, and is present in prokaryotes, eukaryotes, and archaea. The enzymes differ in substrate preference and reaction chemistry, a factor that precludes their classification by homology studies and electronic annotation schemes alone. In this work, I propose and explore the rationale of using substrates to classify structurally similar alpha-ketoglutarate dependent enzymes. Differential catalysis in phylogenetic clades of 2-OG dependent enzymes, is determined by the interactions of a subset of active-site amino acids. Identifying these with existing computational methods is challenging and not feasible for all proteins. A clustering protocol based on validated mechanisms of catalysis of known molecules, in tandem with group specific hidden markov model profiles is able to differentiate and sequester these enzymes. Access to this repository is by a web server that compares user defined unknown sequences to these pre-defined profiles and outputs a list of predicted catalytic domains. The server is free and is accessible at the following URL ( http://comp-biol.theacms.in/H2OGpred.html). The proposed stratification is a novel attempt at classifying and predicting 2-oxoglutarate dependent function. In addition, the server will provide researchers with a tool to compare their data to a comprehensive list of HMM profiles of catalytic domains. This work, will aid efforts by investigators to screen and characterize putative 2-OG dependent sequences. The profile database will be updated at regular intervals.