Safo Martin K, Musayev Faik N, Hunt Sharyn, di Salvo Martino L, Scarsdale Neel, Schirch Verne
Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA 23219, USA .
J Bacteriol. 2004 Dec;186(23):8074-82. doi: 10.1128/JB.186.23.8074-8082.2004.
The crystal structure of Escherichia coli PdxY, the protein product of the pdxY gene, has been determined to a 2.2-A resolution. PdxY is a member of the ribokinase superfamily of enzymes and has sequence homology with pyridoxal kinases that phosphorylate pyridoxal at the C-5' hydroxyl. The protein is a homodimer with an active site on each monomer composed of residues that come exclusively from each respective subunit. The active site is filled with a density that fits that of pyridoxal. In monomer A, the ligand appears to be covalently attached to Cys122 as a thiohemiacetal, while in monomer B it is not covalently attached but appears to be partially present as pyridoxal 5'-phosphate. The presence of pyridoxal phosphate and pyridoxal as ligands was confirmed by the activation of aposerine hydroxymethyltransferase after release of the ligand by the denaturation of PdxY. The ligand, which appears to be covalently attached to Cys122, does not dissociate after denaturation of the protein. A detailed comparison (of functional properties, sequence homology, active site and ATP-binding-site residues, and active site flap types) of PdxY with other pyridoxal kinases as well as the ribokinase superfamily in general suggested that PdxY is a member of a new subclass of the ribokinase superfamily. The structure of PdxY also permitted an interpretation of work that was previously published about this enzyme.
已确定大肠杆菌pdxY基因的蛋白质产物PdxY的晶体结构，分辨率达到2.2埃。PdxY是核糖激酶超家族酶的成员，与在C-5'羟基处磷酸化吡哆醛的吡哆醛激酶具有序列同源性。该蛋白质是一种同型二聚体，每个单体上都有一个活性位点，该活性位点由仅来自各自亚基的残基组成。活性位点充满了与吡哆醛相匹配的密度。在单体A中，配体似乎以硫代半缩醛的形式与Cys122共价连接，而在单体B中，它不是共价连接的，但似乎部分以吡哆醛5'-磷酸的形式存在。通过PdxY变性释放配体后，对磷酸吡哆醛羟甲基转移酶的激活证实了磷酸吡哆醛和吡哆醛作为配体的存在。似乎与Cys122共价连接的配体在蛋白质变性后不会解离。对PdxY与其他吡哆醛激酶以及一般核糖激酶超家族的功能特性、序列同源性、活性位点和ATP结合位点残基以及活性位点侧翼类型进行详细比较表明，PdxY是核糖激酶超家族一个新亚类的成员。PdxY的结构也有助于解释先前发表的关于这种酶的研究工作。
