Tahanejad F S, Naderi-Manesh H, Habibinejad B, Mahmoudian M
Department of Pharmacology, Baghiyatollah University of Medical Sciences, P.O. Box: 19585-698, Tehran, Iran.
Eur J Med Chem. 2000 Jun;35(6):567-76. doi: 10.1016/s0223-5234(00)00155-0.
The 3-D structural information is a prerequisite for a rational ligand design. In the absence of experimental data, model building on the basis of a known 3-D structure of a homologous protein is at present the only reliable method to obtain structural information. A homology model building study of the pyridoxal 5'-phosphate (PLP)-dependent histidine decarboxylase from Morganella morganii (HDC-MM) has been carried out based on the crystal structure of the aspartate aminotransferase from Escherichia coli (AAT-EC). The primary sequences of AAT-EC and HDC-MM were aligned by automated alignment procedure. A 3-D model of HDC-MM was constructed by copying the coordinates of the residues from the crystal structure of AAT-EC into the corresponding residues in HDC-MM. After energy-minimization of the resulting 3-D model of HDC-MM, possible active site residues were identified by fitting the substrate (l-histidine) into the proposed active-site. In our model, several residues, which have an important role in the AAT-EC active-site, are located in positions spatially identical to those in AAT-EC structure. The back-bone of the modelled active site pocket is constructed by residues; Gly-92, Gly-93, Thr-93, Ser-115, Asp-200, Ala-202, Ser-229 and Lys-232 together with residues Asn-8, His-119, Thr-171, His-198, Leu-203, His-231, Ser-236 and Ile-238. In the ligand binding site, it appears that the HDC-MM model will position l-histidine (substrate) in the area consisting of the residues; Glu-29, Ser-30, Leu-38, His-231 and Lys-232. The nitrogen atom of the imidazole ring (N2) of the substrate is predicted to interact with the carboxylate group of Ser-30. The alpha-carboxylate of histidine points toward the Lys-232 to have electrostatic interaction with its side chain nitrogen atom (N(Z)). In conclusion, this combination of sequence and 3-D structural homology between AAT-EC and HDC-MM model could provide insight in assigning the probable active site residues.
三维结构信息是合理进行配体设计的前提条件。在缺乏实验数据的情况下，基于同源蛋白质已知的三维结构进行模型构建是目前获取结构信息的唯一可靠方法。已基于大肠杆菌天冬氨酸转氨酶（AAT-EC）的晶体结构，对摩根氏摩根菌的磷酸吡哆醛（PLP）依赖性组氨酸脱羧酶（HDC-MM）开展了同源性模型构建研究。通过自动比对程序对AAT-EC和HDC-MM的一级序列进行了比对。通过将AAT-EC晶体结构中残基的坐标复制到HDC-MM的相应残基中，构建了HDC-MM的三维模型。在对所得的HDC-MM三维模型进行能量最小化处理后，通过将底物（L-组氨酸）拟合到所提出的活性位点中来确定可能的活性位点残基。在我们的模型中，在AAT-EC活性位点中起重要作用的几个残基，位于与AAT-EC结构中空间位置相同的位点。建模的活性位点口袋的主链由以下残基构成：Gly-92、Gly-93、Thr-93、Ser-115、Asp-200、Ala-202、Ser-229和Lys-232，以及残基Asn-8、His-119、Thr-171、His-198、Leu-203、His-231、Ser-236和Ile-238。在配体结合位点，HDC-MM模型似乎会将L-组氨酸（底物）定位在由以下残基组成的区域：Glu-29、Ser-30、Leu-38、His-231和Lys-232。预计底物咪唑环的氮原子（N2）会与Ser-30的羧基相互作用。组氨酸的α-羧基指向Lys-232，以便与其侧链氮原子（N(Z)）发生静电相互作用。总之，AAT-EC与HDC-MM模型之间的序列和三维结构同源性的这种结合，可为确定可能的活性位点残基提供见解。
