A standard numbering scheme for thiamine diphosphate-dependent decarboxylases
A standard numbering scheme for thiamine diphosphate-dependent decarboxylases
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DOI：
10.1186/1471-2091-13-24
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发表时间：
2012-11-17
期刊：
影响因子：
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通讯作者：
Pleiss, Juergen
中科院分区：
文献类型：
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作者：
Vogel, Constantin;Widmann, Michael;Pleiss, Juergen
背景资料：同源蛋白质家族的标准编号方案允许明确鉴定功能和结构相关残基，交流突变结果，并系统地分析蛋白质家族中的序列-功能关系。标准编号方案已经成功地用于几个蛋白质家族，包括内酰胺酶和抗体，而用于硫胺素-二磷酸（ThDP）依赖性脱羧酶的结构家族的编号方案，ThDP依赖性酶类别的一个大亚家族，包括丙酮酸-、苯甲酰甲酸-、2-含氧酸-、吲哚丙酮酸-和苯丙酮酸脱羧酶，苯甲醛裂解酶，乙酰羟酸脱氢酶和2-琥珀酰基-5-烯醇基-6-羟基-3-环己二烯-1-羧酸合酶（MenD）仍然缺失。尽管ThDP依赖的脱羧酶的成员之间的结构相似性很高，它们的序列是不同的，使成对的序列比较的蛋白质家族members difficult.Results：我们开发和验证了一个标准的编号方案的ThDP依赖的脱羧酶家族。使用来自ThDP依赖性脱羧酶家族的一组代表性序列创建概况隐马尔可夫模型（HMM）。对S.选择酿酒酵母（PDB：2 VK 8）作为参照，因为它是一种充分表征的酶。PDB标识符为2 VK 8的晶体结构包括ScPDC突变体E477 Q、辅因子ThDP和Mg 2+以及底物类似物（2S）-2-羟基丙酸的结构。将该参考序列的绝对编号转移至ThDP依赖性脱羧酶蛋白家族的所有成员。随后，编号方案被集成到已经建立的硫胺素二磷酸依赖酶工程数据库（TEED），并用于系统地分析功能和结构相关的位置在超家族的ThDP依赖decarboxylases.Conclusions：编号方案作为一种工具，为可靠的序列比对的ThDP依赖的decarboxylases和明确的识别和通信相应的位置。因此，它是系统和自动化分析序列编码的特性，如氨基酸位置的结构和功能相关性的基础，因为保守位置的分析，相关突变的鉴定和亚家族特异性氨基酸分布的确定依赖于可靠的多序列比对和比对列的明确鉴定。该方法是可靠和稳健的，并且可以容易地适应于其他蛋白质家族。
Background: Standard numbering schemes for families of homologous proteins allow for the unambiguous identification of functionally and structurally relevant residues, to communicate results on mutations, and to systematically analyse sequence-function relationships in protein families. Standard numbering schemes have been successfully implemented for several protein families, including lactamases and antibodies, whereas a numbering scheme for the structural family of thiamine-diphosphate (ThDP) -dependent decarboxylases, a large subfamily of the class of ThDP-dependent enzymes encompassing pyruvate-, benzoylformate-, 2-oxo acid-, indolpyruvate- and phenylpyruvate decarboxylases, benzaldehyde lyase, acetohydroxyacid synthases and 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase (MenD) is still missing. Despite a high structural similarity between the members of the ThDP-dependent decarboxylases, their sequences are diverse and make a pairwise sequence comparison of protein family members difficult.Results: We developed and validated a standard numbering scheme for the family of ThDP-dependent decarboxylases. A profile hidden Markov model (HMM) was created using a set of representative sequences from the family of ThDP-dependent decarboxylases. The pyruvate decarboxylase from S. cerevisiae (PDB: 2VK8) was chosen as a reference because it is a well characterized enzyme. The crystal structure with the PDB identifier 2VK8 encompasses the structure of the ScPDC mutant E477Q, the cofactors ThDP and Mg2+ as well as the substrate analogue (2S)-2-hydroxypropanoic acid. The absolute numbering of this reference sequence was transferred to all members of the ThDP-dependent decarboxylase protein family. Subsequently, the numbering scheme was integrated into the already established Thiamine-diphosphate dependent Enzyme Engineering Database (TEED) and was used to systematically analyze functionally and structurally relevant positions in the superfamily of ThDP-dependent decarboxylases.Conclusions: The numbering scheme serves as a tool for the reliable sequence alignment of ThDP-dependent decarboxylases and the unambiguous identification and communication of corresponding positions. Thus, it is the basis for the systematic and automated analysis of sequence-encoded properties such as structural and functional relevance of amino acid positions, because the analysis of conserved positions, the identification of correlated mutations and the determination of subfamily specific amino acid distributions depend on reliable multisequence alignments and the unambiguous identification of the alignment columns. The method is reliable and robust and can easily be adapted to further protein families.