Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition
Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition
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DOI：
10.1073/pnas.1703663114
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发表时间：
2017-09-26
影响因子：
11.1
通讯作者：
Ando, Nozomi
中科院分区：
文献类型：
--
作者：
Davis, Katherine M.;Schramma, Kelsey R.;Ando, Nozomi
核糖体合成肽的翻译后修饰为生产称为 RiPP（核糖体合成和翻译后修饰肽）的生物活性分子提供了一种优雅的方法。尽管前体肽的前导序列通常是周转所必需的，但对于此类天然产物的许多成员来说，修饰酶的确切识别模式仍不清楚。在这里，我们使用 X 射线晶体学和计算模型来研究前导肽在链肽同系物生物合成中的作用，链肽是一种最近鉴定的肽天然产物，具有分子内赖氨酸-色氨酸交联，由自由基 S-腺苷甲硫氨酸 (SAM) 酶 StrB 安装。我们展示了 SuiB（StrB 的密切直系同源物）的各种形式的晶体结构，包括载脂蛋白 SuiB、SAM 结合的 SuiB 以及 SuiB 与 SAM 及其肽底物 SuiA 的复合物。尽管 SuiB 的 N 端结构域采用典型的 RRE（RiPP 识别元件）基序，该基序与前体肽识别有关，但我们观察到前导肽在催化桶中而不是 N 端结构域中结合。计算模拟支持一种机制，其中前导肽通过将前体肽的交联残基定位在活性位点内来引导翻译后修饰。这些结果共同揭示了前体肽的结合以及天然产物链肽家族中形成独特碳-碳交联所需的相关构象变化。
Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. Here, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine-tryptophan cross-link, which is installed by the radical S-adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon-carbon cross-link in the streptide family of natural products.