Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains
Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains
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DOI：
10.1016/s1074-5521(00)00091-0
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发表时间：
2000-03-01
影响因子：
--
通讯作者：
Townsend, CA
中科院分区：
文献类型：
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作者：
Challis, GL;Ravel, J;Townsend, CA
背景：非核糖体肽合成酶（NRPSs）是一种大的模块化蛋白质，可以选择性地以有序的方式结合、激活和浓缩氨基酸。底物识别和激活发生在每个模块的腺苷化(A)域内与ATP反应。最近，gramicidin合成酶（GrsA）与l -苯丙氨酸和单磷酸腺苷结合的A结构域的晶体结构被确定。结果：所有已知NRPS A结构域的关键残基都与GrsA A结构域的8个结合袋残基一致，并定义了一组非常保守的识别模板。这些组之间的系统发育关系以及极性和非极性氨基酸的可能特异性决定因素是根据广泛发表的这些酶的生化数据确定的。超过80%的已知NRPS A结构域的结合特异性与30多种氨基酸底物相关。结论：所提出的分析可以预测未知功能的A结构域的特异性（例如，聚合酶链反应扩增或基因组测序）。此外，它为通过位点定向诱变改变a结构域特异性提供了一个合理的框架，这在新的天然产物的生物合成工程中具有重要的潜力。
Background: Nonribosomal peptide synthetases (NRPSs) are large modular proteins that selectively bind, activate and condense amino acids in an ordered manner. Substrate recognition and activation occurs by reaction with ATP within the adenylation (A) domain of each module. Recently, the crystal structure of the A domain from the gramicidin synthetase (GrsA) with L-phenylalanine and adenosine monophosphate bound has been determined.Results: Critical residues in all known NRPS A domains have been identified that align with eight binding-pocket residues in the GrsA A domain and define sets of remarkably conserved recognition templates. Phylogenetic relationships among these sets and the likely specificity determinants for polar and nonpolar amino acids were determined in light of extensive published biochemical data for these enzymes. The binding specificity of greater than 80% of the known NRPS A domains has been correlated with more than 30 amino acid substrates.Conclusions: The analysis presented allows the specificity of A domains of unknown function (e.g. from polymerase chain reaction amplification or genome sequencing) to be predicted. Furthermore, it provides a rational framework for altering of A domain specificity by site-directed mutagenesis, which has significant potential for engineering the biosynthesis of novel natural products.