A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer.
A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer.
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DOI：
10.7554/elife.81547
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发表时间：
2023-01-11
期刊：
影响因子：
7.7
通讯作者：
Van Der Woude MW
中科院分区：
文献类型：
--
作者：
Newman KE;Tindall SN;Mader SL;Khalid S;Thomas GH;Van Der Woude MW
不同的碳水化合物的酰化作用存在于生命的所有区域，并且可以被带有膜结合的酰基转移酶-3(AT3)结构域的蛋白质(PF01757)催化。在细菌中，这些蛋白质在共生、对病毒和抗菌剂的抵抗以及抗生素的生物合成等过程中是必不可少的，但它们的结构和机制在很大程度上是未知的。在这项研究中，进化协方差分析被用来建立细菌O抗原修饰的乙酰转移酶OafB的结构的计算模型。得到的结构显示了AT3结构域的新折叠，分子动力学模拟表明该折叠在膜中是稳定的。AT3结构域包含10个跨膜螺旋，它们排列成一个巨大的细胞质空腔，里面排列着已知对功能至关重要的残基。进一步的分子动力学模拟支持这样一个模型，即酰基-CoA供体通过访问由覆盖内腔的重要环的移动而产生的孔来跨越膜，从而使OafB能够将乙酰基呈现在细胞质外表面上可能的催化位置附近。与OafB中融合的SGNH结构域的有限但重要的相互作用被确定，模拟表明该结构域是可移动的，既可以接受AT3的酰基，又可以到达膜外的受体底物。总之，这种新的AT3功能的通用模型为开发能够消除细菌病原体的关键功能的抑制剂提供了一个框架。包围细胞的脂肪膜是所有生物的基本特征。它是一种选择性屏障，只允许某些物质进入和离开细胞，它含有细胞用来与环境相互作用的蛋白质和碳水化合物。在细菌中，细胞膜外层的碳水化合物可以被标记或修饰成小的化学物质，这通常被证明对细胞有用。例如，酰基允许致病细菌逃避免疫系统，导致感染在体内持续存在。一般来说，激活的酰基只在细胞内发现，所以它们需要跨膜移动，然后才能连接到表面的碳水化合物上。这种转移是由一组位于膜内的蛋白质执行的，这些蛋白质被称为酰基转移酶-3(AT3)家族。这些蛋白质的结构和它们促进膜交叉的机制尚不清楚。Newman、Tindall等人的研究成果。将计算和结构建模技术与现有的实验数据相结合，以确定这一蛋白质家族如何在膜上移动酰基。他们把重点放在OafB上，这是一种来自食源性致病菌鼠伤寒沙门氏菌的AT3蛋白。研究小组使用的实验数据包括有关这种蛋白质酰化碳水化合物分子所必需的OafB部分的信息。在他们的实验中，纽曼、廷德尔等人。研究了OafB的不同部分如何移动，它们如何与将酰基带到膜上的分子相互作用，以及酰基如何转移到碳水化合物受体。他们的结果表明，AT3家族蛋白有一个中心孔或洞，被一个环堵塞。这个环路移动，因此“拔出”毛孔，导致出现一个横跨膜的通道。这个通道可以容纳酰基供体分子，将酰基呈现到膜的外表面，在那里它可以转移到受体碳水化合物。AT3蛋白家族参与了许多涉及膜的细胞过程，一系列细菌病原体依赖这些蛋白成功感染人类宿主。Newman Tindall等人的结果。因此，可以在生物科学中使用，以提供对膜的更详细的了解，并为抗击细菌疾病的药物的设计提供信息。
Acylation of diverse carbohydrates occurs across all domains of life and can be catalysed by proteins with a membrane bound acyltransferase-3 (AT3) domain (PF01757). In bacteria, these proteins are essential in processes including symbiosis, resistance to viruses and antimicrobials, and biosynthesis of antibiotics, yet their structure and mechanism are largely unknown. In this study, evolutionary co-variance analysis was used to build a computational model of the structure of a bacterial O-antigen modifying acetyltransferase, OafB. The resulting structure exhibited a novel fold for the AT3 domain, which molecular dynamics simulations demonstrated is stable in the membrane. The AT3 domain contains 10 transmembrane helices arranged to form a large cytoplasmic cavity lined by residues known to be essential for function. Further molecular dynamics simulations support a model where the acyl-coA donor spans the membrane through accessing a pore created by movement of an important loop capping the inner cavity, enabling OafB to present the acetyl group close to the likely catalytic resides on the extracytoplasmic surface. Limited but important interactions with the fused SGNH domain in OafB are identified, and modelling suggests this domain is mobile and can both accept acyl-groups from the AT3 and then reach beyond the membrane to reach acceptor substrates. Together this new general model of AT3 function provides a framework for the development of inhibitors that could abrogate critical functions of bacterial pathogens. The fatty membrane that surrounds cells is an essential feature of all living things. It is a selective barrier, only allowing certain substances to enter and exit the cell, and it contains the proteins and carbohydrates that the cell uses to interact with its environment. In bacteria, the carbohydrates on the outer side of the membrane can become ‘tagged’ or modified with small chemical entities which often prove useful for the cell. Acyl groups, for example, allow disease-causing bacteria to evade the immune system and contribute to infections persisting in the body. As a rule, activated acyl groups are only found inside the cell, so they need to move across the membrane before they can be attached onto the carbohydrates at the surface. This transfer is performed by a group of proteins that sit within the membrane called the acyltransferase-3 (AT3) family. The structure of these proteins and the mechanism by which they facilitate membrane crossing have remained unclear. Newman, Tindall et al. combined computational and structural modelling techniques with existing experimental data to establish how this family of proteins moves acyl groups across the membrane. They focused on OafB, an AT3 protein from the foodborne bacterial pathogen Salmonella typhimurium. The experimental data used by the team included information about which parts of OafB are necessary for this protein to acylate carbohydrates molecules. In their experiments, Newman, Tindall et al. studied how different parts of OafB move, how they interact with the molecules that carry an acyl group to the membrane, and how the acyl group is then transferred to the carbohydrate acceptor. Their results suggest that AT3 family proteins have a central pore or hole, plugged by a loop. This loop moves and therefore ‘unplug’ the pore, resulting in the emergence of a channel across the membrane. This channel can accommodate the acyl-donating molecule, presenting the acyl group to the outer surface of the membrane where it can be transferred to the acceptor carbohydrate. The AT3 family of proteins participates in many cellular processes involving the membrane, and a range of bacterial pathogens rely on these proteins to successfully infect human hosts. The results of Newman Tindall et al. could therefore be used across the biological sciences to provide more detailed understanding of the membrane, and to inform the design of drugs to fight bacterial diseases.
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