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首页> 外文期刊>Journal of Molecular Biology >Functional attributes of the phosphate group binding cup of pyridoxal phosphate-dependent enzymes.
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Functional attributes of the phosphate group binding cup of pyridoxal phosphate-dependent enzymes.

机译：吡ido醛磷酸依赖性酶的磷酸基结合杯的功能属性。

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摘要

Twenty-four structures of pyridoxal-5'-phosphate (PLP)-dependent enzymes that represent five different folds are shown to share a common recognition pattern for the phosphate group of their PLP-ligands. All atoms that interact with the phosphate group of PLP in these proteins are organized within a two-layer structure so that the first interacting layer contains from five to seven atoms and parallel with this is a second layer containing from three to seven interacting atoms. In order to identify features of the phosphate-binding site common to PLP-dependent enzymes, a simple procedure is described that assigns relative positions to all interacting atoms unambiguously, such that the networks of interactions for different proteins can be compared. On the basis of these diagrams for 24 enzyme-cofactor complexes, a detailed comparison of the two-layer structures of PLP-dependent enzymes, with both similar and different folds, was made. A majority of the structurally defined PLP-dependent proteins use the same atom types in analogous "key" positions to bind their PLP-ligands. In some instances, proteins use water molecules when a key position is unoccupied. A similar two-layer recognition pattern extends to protein recognition of at least one other, non-PLP ligand, glucosamine 6-phosphate. We refer to this three-dimensional recognition pattern as the phosphate-binding cup. In general, the phosphate-binding cup provides a very stable anchoring point for PLP. When numerous water molecules occur within the cup, however, then the phosphate group of PLP participates directly in the enzymatic reactions with inorganic phosphate replacing the water molecules of the cup. With glucosamine-6-phosphate synthase, the water molecules of the phosphate-binding cup facilitate the entry of substrate and the exit of product.
机译：吡咯醛5'-磷酸（PLP）依赖性酶的二十四个结构代表了五个不同的折叠，显示它们的PLP配体的磷酸基具有相同的识别模式。这些蛋白质中与PLP磷酸基团相互作用的所有原子都组织成两层结构，因此第一相互作用层包含5至7个原子，与此平行的第二层则包含3至7个相互作用原子。为了鉴定PLP依赖性酶共有的磷酸结合位点的特征，描述了一种简单的程序，该程序明确地为所有相互作用的原子分配了相对位置，从而可以比较不同蛋白质的相互作用网络。根据这些图对24种酶-辅因子复合物，对具有相似和不同倍数的PLP依赖性酶的两层结构进行了详细比较。大多数结构定义的PLP依赖性蛋白在相似的“关键”位置使用相同的原子类型来结合其PLP配体。在某些情况下，当关键位置未被占用时，蛋白质会使用水分子。类似的两层识别模式可扩展到至少一种其他非PLP配体，6-磷酸氨基葡萄糖的蛋白质识别。我们将此三维识别模式称为磷酸盐结合杯。通常，磷酸盐结合杯可为PLP提供非常稳定的固定点。但是，当杯子中出现大量水分子时，PLP的磷酸基团将直接参与酶促反应，而无机磷酸盐会取代杯子中的水分子。用6-磷酸氨基葡萄糖合成酶，磷酸盐结合杯的水分子有助于底物的进入和产物的排出。

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