Structural basis for peptide recognition by archaeal oligopeptide permease A
Structural basis for peptide recognition by archaeal oligopeptide permease A
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DOI：
10.1002/prot.26324
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发表时间：
2022-02
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通讯作者：
H. Yokoyama;N. Kamei;Keijiro Konishi;K. Hara;Y. Ishikawa;I. Matsui;P. Forterre;H. Hashimoto
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作者：
H. Yokoyama;N. Kamei;Keijiro Konishi;K. Hara;Y. Ishikawa;I. Matsui;P. Forterre;H. Hashimoto
寡肽通透酶A（OppA）在细胞的营养和各种信号转导过程中起着重要作用。在古细菌中，OppA是存在于热球菌属的膜囊泡中的主要蛋白质。由于迄今为止还没有确定古菌OppA的晶体结构，我们通过单波长异常色散方法在2.3 nm分辨率下报告了来自Thermococcus kodakaraensis（TkOppA）的古菌OppA的晶体结构。TkOppA由与细菌OppA类似的三个结构域组成，并且细菌OppA中不存在的插入区域位于核心区域的外围。内源性五肽通过肽主链原子的氢键和疏水相互作用结合在TkOppA结构域I和III的口袋中。未观察到肽侧链原子的氢键;因此，TkOppA可能具有低肽选择性，但对残基2和3具有一定的偏好。TkOppA具有相对较大的口袋，可以结合九肽;因此，与革兰氏阳性菌的OppA类似，它适用于结合大肽。
Oligopeptide permease A (OppA) plays an important role in the nutrition of cells and various signaling processes. In archaea, OppA is a major protein present in membrane vesicles of Thermococcales. Because there being no crystal structures of archaeal OppAs determined to date, we report the crystal structure of archaeal OppA from Thermococcus kodakaraensis (TkOppA) at 2.3 Å resolution by the single‐wavelength anomalous dispersion method. TkOppA consists of three domains similarly to bacterial OppAs, and the inserted regions not present in bacterial OppAs are at the periphery of the core region. An endogenous pentapeptide was bound in the pocket of domains I and III of TkOppA by hydrogen bonds of main‐chain atoms of the peptide and hydrophobic interactions. No hydrogen bonds of side‐chain atoms of the peptide were observed; thus, TkOppA may have low peptide selectivity but some preference for residues 2 and 3. TkOppA has a relatively large pocket and can bind a nonapeptide; therefore, it is suitable for the binding of large peptides similarly to OppAs of Gram‐positive bacteria.