Molecular basis of substrate selection by the N-end rule adaptor protein ClpS
Molecular basis of substrate selection by the N-end rule adaptor protein ClpS
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DOI：
10.1073/pnas.0903614106
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发表时间：
2009-06
期刊：
影响因子：
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通讯作者：
G. Román-Hernández;R. Grant;R. Sauer;T. Baker
中科院分区：
文献类型：
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作者：
G. Román-Hernández;R. Grant;R. Sauer;T. Baker
N-末端规则是一种保守的降解途径，其将蛋白质的稳定性与其N-末端氨基酸联系起来。在这里，我们展示了细菌N端规则衔接子ClpS的晶体结构，单独与含有N端苯丙氨酸、亮氨酸和色氨酸的肽结合。这些结构，连同以前的结构ClpS绑定到一个N-末端酪氨酸，说明了一套完整的初级N-末端规则氨基酸的分子基础的识别。在每种情况下，N-末端残基的α-氨基和侧链是识别的主要决定因素。N-末端残基的结合口袋在游离衔接子中预先形成，并且仅需要小的调整以适应具有基本上不同的大小和形状的N-末端规则残基。已知M53 A ClpS介导底物的扩展库的降解，包括具有N-末端缬氨酸或异亮氨酸的那些。与N-末端规则色氨酸接合的Met 53 A ClpS的结构揭示了基本上野生型的识别机制，表明Met 53侧链通过与β-分支侧链冲突并排除β-分支侧链而直接实施特异性。最后，实验和结构数据表明的机制，使蛋白质与N-末端甲硫氨酸结合非常差的ClpS，解释了为什么这些高丰度的蛋白质不通过N-末端规则途径在细胞中降解。
The N-end rule is a conserved degradation pathway that relates the stability of a protein to its N-terminal amino acid. Here, we present crystal structures of ClpS, the bacterial N-end rule adaptor, alone and engaged with peptides containing N-terminal phenylalanine, leucine, and tryptophan. These structures, together with a previous structure of ClpS bound to an N-terminal tyrosine, illustrate the molecular basis of recognition of the complete set of primary N-end rule amino acids. In each case, the α-amino group and side chain of the N-terminal residue are the major determinants of recognition. The binding pocket for the N-end residue is preformed in the free adaptor, and only small adjustments are needed to accommodate N-end rule residues having substantially different sizes and shapes. M53A ClpS is known to mediate degradation of an expanded repertoire of substrates, including those with N-terminal valine or isoleucine. A structure of Met53A ClpS engaged with an N-end rule tryptophan reveals an essentially wild-type mechanism of recognition, indicating that the Met53 side chain directly enforces specificity by clashing with and excluding β-branched side chains. Finally, experimental and structural data suggest mechanisms that make proteins with N-terminal methionine bind very poorly to ClpS, explaining why these high-abundance proteins are not degraded via the N-end rule pathway in the cell.