Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases
Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases
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DOI：
10.1016/s0022-2836(03)00232-8
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发表时间：
2003-04-25
影响因子：
5.6
通讯作者：
Mohanty, B
中科院分区：
文献类型：
--
作者：
Yadav, G;Gokhale, RS;Mohanty, B
模块化聚酮合酶（PKS）是大型多酶、多域巨合酶，参与一类药学上重要的天然产物（即聚酮化合物）的生物合成。这些酶具有一组称为模块的重复活性位点，每个模块中存在的结构域决定了将添加到不断增长的聚酮化合物链中的化学部分。这种生物合成的模块化逻辑已被成功利用，通过基因操作生产几种新型化合物。然而，为了利用其组合生物合成的巨大潜力，有必要开发基于计算机方法的知识，将 PKS 的序列和结构域组织与其聚酮化合物产品相关联。在这项工作中，我们对实验表征的 PKS 簇进行了广泛的序列分析，以开发一种自动计算协议，用于明确识别多肽序列中的各种 PKS 结构域。基于结构的方法已用于识别酰基转移酶（AT）结构域的假定活性位点残基，这些残基控制聚酮化合物生物合成过程中各种起始剂和延伸剂单元的特异性。在对代表性 AT 结构域活性位点残基的分析和对底物的分子建模的基础上，我们鉴定了一个关键残基，该残基可能在通过该结构域选择延伸基团期间区分丙二酸和甲基丙二酸中发挥主要作用。结构模型还解释了实验观察到的 AT 结构域在底物选择中的手性偏好。该计算协议已用于预测来自各种微生物基因组的 PKS 簇的域组织和底物特异性。我们的分析结果以及用于预测结构域组织和底物特异性的计算工具已以可搜索计算机化数据库（PKSDB）的形式组织。 PKSDB 将作为鉴定由未表征的 PKS 簇生物合成的聚酮化合物产品的宝贵工具。该数据库还可以为设计新型聚酮匕首的实验的合理设计提供指导。 (C) 2003 Elsevier Science Ltd. 保留所有权利。
Modular polyketide synthases (PKSs) are large multi-enzymatic, multidomain megasynthases, which are involved in the biosynthesis of a class of pharmaceutically important natural products, namely polyketides. These enzymes harbor a set of repetitive active sites termed modules and the domains present in each module dictate the chemical moiety that would add to a growing polyketide chain. This modular logic of biosynthesis has been exploited with reasonable success to produce several novel compounds by genetic manipulation. However, for harnessing their vast potential of combinatorial biosynthesis, it is essential to develop knowledge based in silico approaches for correlating the sequence and domain organization of PKSs to their polyketide products. In this work, we have carried out extensive sequence analysis of experimentally characterized PKS clusters to develop an automated computational protocol for unambiguous identification of various PKS domains in a polypeptide sequence. A structure based approach has been used to identify the putative active site residues of acyltransferase (AT) domains, which control the specificities for various starter and extender units during polyketide biosynthesis. On the basis of the analysis of the active site residues and molecular modelling of substrates in the active site of representative AT domains, we have identified a crucial residue that is likely to play a major role in discriminating between malonate and methylmalonate during selection of extender groups by this domain. Structural modelling has also explained the experimentally observed chiral preference of AT domain in substrate selection. This computational protocol has been used to predict the domain organization and substrate specificity for PKS clusters from various microbial genomes. The results of our analysis as well as the computational tools for prediction of domain organization and substrate specificity have been organized in the form of a searchable computerized database (PKSDB). PKSDB would serve as a valuable tool for identification of polyketide products biosynthesized by uncharacterized PKS clusters. This database can also provide guidelines for rational design of experiments to engineer novel polyketidesdagger. (C) 2003 Elsevier Science Ltd. All rights reserved.