大肠杆菌 DNA 聚合酶调控蛋白 UmuD 和 UmuD'的构象动力学。

Conformational dynamics of the Escherichia coli DNA polymerase manager proteins UmuD and UmuD'.

机构信息

Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.

出版信息

J Mol Biol. 2010 Apr 23;398(1):40-53. doi: 10.1016/j.jmb.2010.02.040. Epub 2010 Mar 4.

Abstract

The expression of Escherichia coli umuD gene products is upregulated as part of the SOS response to DNA damage. UmuD is initially produced as a 139-amino-acid protein, which subsequently cleaves off its N-terminal 24 amino acids in a reaction dependent on RecA/single-stranded DNA, giving UmuD'. The two forms of the umuD gene products play different roles in the cell. UmuD is implicated in a primitive DNA damage checkpoint and prevents DNA polymerase IV-dependent -1 frameshift mutagenesis, while the cleaved form facilitates UmuC-dependent mutagenesis via formation of DNA polymerase V (UmuD'(2)C). Thus, the cleavage of UmuD is a crucial switch that regulates replication and mutagenesis via numerous protein-protein interactions. A UmuD variant, UmuD3A, which is noncleavable but is a partial biological mimic of the cleaved form UmuD', has been identified. We used hydrogen-deuterium exchange mass spectrometry (HXMS) to probe the conformations of UmuD, UmuD', and UmuD3A. In HXMS experiments, backbone amide hydrogens that are solvent accessible or not involved in hydrogen bonding become labeled with deuterium over time. Our HXMS results reveal that the N-terminal arm of UmuD, which is truncated in the cleaved form UmuD', is dynamic. Residues that are likely to contact the N-terminal arm show more deuterium exchange in UmuD' and UmuD3A than in UmuD. These observations suggest that noncleavable UmuD3A mimics the cleaved form UmuD' because, in both cases, the arms are relatively unbound from the globular domain. Gas-phase hydrogen exchange experiments, which specifically probe the exchange of side-chain hydrogens and are carried out on shorter timescales than solution experiments, show that UmuD' incorporates more deuterium than either UmuD or UmuD3A. This work indicates that these three forms of the UmuD gene products are highly flexible, which is of critical importance for their many protein interactions.

摘要

大肠杆菌 umuD 基因产物的表达作为 DNA 损伤的 SOS 反应的一部分上调。UmuD 最初作为 139 个氨基酸的蛋白质产生,随后在依赖 RecA/单链 DNA 的反应中从其 N 端切除 24 个氨基酸,得到 UmuD'。两种形式的 umuD 基因产物在细胞中发挥不同的作用。UmuD 参与原始的 DNA 损伤检查点,并防止 DNA 聚合酶 IV 依赖性-1 移框诱变,而切割形式通过形成 DNA 聚合酶 V(UmuD'(2)C)促进 UmuC 依赖性诱变。因此,UmuD 的切割是通过多种蛋白质-蛋白质相互作用调节复制和诱变的关键开关。已经鉴定出一种不可切割但部分模拟切割形式 UmuD'的 UmuD 变体 UmuD3A。我们使用氘-氢交换质谱(HXMS)来探测 UmuD、UmuD'和 UmuD3A 的构象。在 HXMS 实验中,随着时间的推移,溶剂可及或不参与氢键的 backbone 酰胺氢逐渐被氘标记。我们的 HXMS 结果表明,在切割形式 UmuD'中被截断的 UmuD 的 N 端臂是动态的。在 UmuD'和 UmuD3A 中可能与 N 端臂接触的残基显示出比 UmuD 更多的氘交换。这些观察结果表明,不可切割的 UmuD3A 模拟切割形式的 UmuD',因为在这两种情况下,臂相对未与球形结构域结合。气相氢交换实验专门探测侧链氢的交换,并且在比溶液实验更短的时间尺度上进行,结果表明 UmuD'比 UmuD 或 UmuD3A 掺入更多的氘。这项工作表明,这三种形式的 UmuD 基因产物具有高度的灵活性,这对于它们的许多蛋白质相互作用至关重要。

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