Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality
Linking enzyme sequence to function using conserved property difference locator to identify and annotate positions likely to control specific functionality
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DOI：
10.1186/1471-2105-6-284
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发表时间：
2005-11-30
影响因子：
3
通讯作者：
Shanklin, J
中科院分区：
文献类型：
--
作者：
Mayer, KM;McCorkle, SR;Shanklin, J
背景：同源酶家族由共同的祖先进化而来。代表每种活性的多个序列的可用性为提取指定单个同系物的功能的信息提供了机会。我们提出了一个简单的方法，用于确定类的特定功能，其中多个序列比对转换为注释的图形形式的保守属性差异的cpdl（CPDL）program.Results：三个测试用例，每个测试用例由两组functionally-distinct同系物，提出了。在测试用例中，一个是膜，两个是可溶性酶家族。去饱和酶/羟化酶数据用于设计和测试CPDL算法，因为比较序列方法已成功应用于操纵这些酶的特异性。选择另外两种情况，ATP/GTP环化酶和MurD/MurE环化酶，因为它们在结构和生物化学上都有很好的特征。对于去饱和酶/羟化酶、ATP/GTP环化酶和MurD/MurE环化酶，8个组（类似于400），4（类似于150）和10（> 400）个感兴趣的残基，其含有经验定义的特异性决定位置。CPDL始终识别酶活性位点附近的位置，包括从结构和/或生化研究预测的对特异性和/或功能重要的位置。这表明，CPDL将具有广泛的实用性，用于基于同源蛋白质组的多序列分析来鉴定潜在的类别决定残基。由于该方法是序列，而不是结构，它同样适合于设计结构功能实验，以研究膜和可溶性蛋白质。
Background: Families of homologous enzymes evolved from common progenitors. The availability of multiple sequences representing each activity presents an opportunity for extracting information specifying the functionality of individual homologs. We present a straightforward method for the identification of residues likely to determine class specific functionality in which multiple sequence alignments are converted to an annotated graphical form by the Conserved Property Difference Locator ( CPDL) program.Results: Three test cases, each comprised of two groups of funtionally-distinct homologs, are presented. Of the test cases, one is a membrane and two are soluble enzyme families. The desaturase/hydroxylase data was used to design and test the CPDL algorithm because a comparative sequence approach had been successfully applied to manipulate the specificity of these enzymes. The other two cases, ATP/GTP cyclases, and MurD/MurE synthases were chosen because they are well characterized structurally and biochemically. For the desaturase/hydroxylase enzymes, the ATP/GTP cyclases and the MurD/MurE synthases, groups of 8 ( of similar to 400), 4 ( of similar to 150) and 10 ( of > 400) residues, respectively, of interest were identified that contain empirically defined specificity determining positions.Conclusion: CPDL consistently identifies positions near enzyme active sites that include those predicted from structural and/or biochemical studies to be important for specificity and/or function. This suggests that CPDL will have broad utility for the identification of potential class determining residues based on multiple sequence analysis of groups of homologous proteins. Because the method is sequence, rather than structure, based it is equally well suited for designing structure-function experiments to investigate membrane and soluble proteins.