Phosphate group binding "cup" of PLP-dependent and non-PLP-dependent enzymes: leitmotif and variations
Phosphate group binding "cup" of PLP-dependent and non-PLP-dependent enzymes: leitmotif and variations
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DOI：
10.1016/s1570-9639(03)00057-8
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发表时间：
2003-04-11
影响因子：
3.2
通讯作者：
Johnson, MS
中科院分区：
文献类型：
--
作者：
Denesyuk, AI;Denessiouk, KA;Johnson, MS
吡哆醛-5′-磷酸（PLP）在氨基酸相互转化的反应中被许多酶广泛使用。虽然吡哆醛环在催化中的作用已被很好地理解，但对单磷酸基团在PLP中的功能作用的研究较少。在这里我们。构建明确的连接图，描述PLP的三个非酯磷酸氧原子与蛋白质结合位点和水分子的周围原子之间的相互作用，即所谓的磷酸基团结合“杯”。这些图提供了一种简单的方法来识别相似和不同蛋白质折叠中磷酸基团的共同识别基序。构建并比较了五种新确定的plp依赖性转移酶（折叠I型酶）结构，以及两种非plp蛋白复合物（吲哚-3-甘油磷酸合成酶（IGPS）与结合的吲哚-3-甘油磷酸（IGP）和结合黄素单核苷酸（FMN）的旧黄酶（OYE））。图的详细比较表明，在磷酸基团结合“杯”的结构中，十个位置中有三个位置包含不变原子，而另外七个位置被保守原子类型占据。在结合三种不同配体：PLP， IGP和FMN的折叠型III （TIM β / α -桶）酶中也观察到这种相似性。(C) 2003 Elsevier Science b.v.版权所有
Pyridoxal-5'-phosphate (PLP) is widely used by many enzymes in reactions where amino acids are interconverted. Whereas the role of the pyridoxal ring in catalysis is well understood, the functional role of the single phosphate group in PLP has been less studied. Here we. construct unambiguous connection diagrams that describe the interactions among the three non-ester phosphate oxygen atoms of PLP and surrounding atoms from the protein binding site and from water molecules, the so-called phosphate group binding "cup". These diagrams provide a simple means to identify common recognition motifs for the phosphate group in both similar and different protein folds. Diagrams were constructed and compared in the cases of five newly determined structures of PLP-dependent transferases (fold type I enzymes) and, additionally, two non-PLP protein complexes (indole-3-glycerol phosphate synthase (IGPS) with bound indole-3-glycerol phosphate (IGP)and old yellow enzyme (OYE) with bound flavin mononucleotide (FMN)). A detailed comparison of the diagrams shows that three positions out of ten in the structure of the phosphate group binding "cup" contain invariant atoms, while seven others are occupied by conserved atom types. This, level of similarity was also observed in the fold type III (TIM beta/alpha-barrel) enzymes that bind three different ligands: PLP, IGP and FMN. (C) 2003 Elsevier Science B.V All rights reserved.