Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer
Structure of NDP-forming Acetyl-CoA synthetase ACD1 reveals a large rearrangement for phosphoryl transfer
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DOI：
10.1073/pnas.1518614113
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发表时间：
2016-01
期刊：
影响因子：
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通讯作者：
R.H.-J. Weisse;A. Faust;Marcel Schmidt;P. Schönheit;A. Scheidig
中科院分区：
文献类型：
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作者：
R.H.-J. Weisse;A. Faust;Marcel Schmidt;P. Schönheit;A. Scheidig
意义 酰基辅酶A硫酯是能量转换的关键底物。相关的 ATP/GTP 合成酶形成一个大的超家族，其成员遍及生命的各个领域。与它们的普遍重要性相反，这些酶的所有步骤的潜在反应机制仍未被了解。在这里，我们描述了来自进化非常古老的古菌的核苷二磷酸形成乙酰辅酶A合成酶的各种结构。观察到酶内发生大的构象重排。该结构揭示了含磷酸组氨酸片段的部分解旋和 120° 重新取向。这种构象重排将酰基辅酶A结合位点与核苷二磷酸结合位点偶联。所提出的结构证明了一个长期存在的假设，并提供了对底物选择性的决定因素的深入了解。形成 NDP 的酰基辅酶 A 合成酶 (ACD) 催化各种辅酶 A 硫酯转化为相应的酸，以 ATP 的形式保存其化学能。 ACD 是超嗜热古菌糖和肽发酵中的主要节能酶。它们被认为是生命早期进化中 ATP 合成的原始酶。据我们所知，我们展示了来自超嗜热古菌 Candidatus Korachaeum cryptofilum 的 ACD 的第一个晶体结构。这些结构揭示了 α2β2-异四聚体复合物中 ACD 亚基 α 和 β 的独特排列。这种安排与该超家族的其他成员显着不同。为了将活化的磷酰基部分从 Ac-CoA 结合位点（α 亚基内）传输到 NDP 结合位点（β 亚基内），必须桥接 51 Å 的距离。这种传输需要在蛋白质复合物内进行更大的重排，涉及 α 亚基的 21 个氨基酸长的含磷酸组氨酸的片段。该片段与 β 亚基相互作用的空间限制解释了 β 亚基内第二个高度保守的 His 残基的必要性。这些数据支持所提出的 ACD 的四步反应机制，即酰基辅酶 A 硫酯与 ATP 合成的偶联。此外，据我们所知，所确定的结合 Ac-CoA 的复合物的晶体结构使我们能够首次了解酰基 CoA 底物特异性的决定因素。突出到酰基辅酶A结合袋中的环的组成和大小由特征子结构域的单独排列决定。
Significance Acyl-CoA thioesters are key substrates for energy conversion. Related ATP/GTP-producing synthetases form a large superfamily with members in all kingdoms of life. In contrast to their general importance, the underlying reaction mechanism of these enzymes is still not understood in all steps. Here, we describe various structures of a nucleoside diphosphate-forming acetyl--CoA synthetase from an evolutionary very old archaeon. A large conformational rearrangement within the enzyme is observed. The structures reveal a partial unwinding and reorientation by 120° of a phosphohistidine-containing segment. This conformational rearrangement couples the acyl-CoA binding site with the nucleoside diphosphate binding site. The presented structures prove a long-standing hypothesis and provide insight into the determinants for substrate selectivity. The NDP-forming acyl-CoA synthetases (ACDs) catalyze the conversion of various CoA thioesters to the corresponding acids, conserving their chemical energy in form of ATP. The ACDs are the major energy-conserving enzymes in sugar and peptide fermentation of hyperthermophilic archaea. They are considered to be primordial enzymes of ATP synthesis in the early evolution of life. We present the first crystal structures, to our knowledge, of an ACD from the hyperthermophilic archaeon Candidatus Korachaeum cryptofilum. These structures reveal a unique arrangement of the ACD subunits alpha and beta within an α2β2-heterotetrameric complex. This arrangement significantly differs from other members of the superfamily. To transmit an activated phosphoryl moiety from the Ac-CoA binding site (within the alpha subunit) to the NDP-binding site (within the beta subunit), a distance of 51 Å has to be bridged. This transmission requires a larger rearrangement within the protein complex involving a 21-aa-long phosphohistidine-containing segment of the alpha subunit. Spatial restraints of the interaction of this segment with the beta subunit explain the necessity for a second highly conserved His residue within the beta subunit. The data support the proposed four-step reaction mechanism of ACDs, coupling acyl-CoA thioesters with ATP synthesis. Furthermore, the determined crystal structure of the complex with bound Ac-CoA allows first insight, to our knowledge, into the determinants for acyl-CoA substrate specificity. The composition and size of loops protruding into the binding pocket of acyl-CoA are determined by the individual arrangement of the characteristic subdomains.