Joseph Raji E, Ginder Nathaniel D, Hoy Julie A, Nix Jay C, Fulton D Bruce, Honzatko Richard B, Andreotti Amy H
Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2012 Feb 1;68(Pt 2):145-53. doi: 10.1107/S1744309111049761. Epub 2012 Jan 25.
The crystal structure of the interleukin-2 tyrosine kinase Src homology domain (Itk SH2) is described and it is found that unlike in studies of this domain using NMR spectroscopy, cis-trans-prolyl isomerization is not readily detected in the crystal structure. Based on similarities between the Itk SH2 crystal form and the cis form of the Itk SH2 NMR structure, it is concluded that it is likely that the prolyl imide bond at least in part adopts the cis conformation in the crystal form. However, the lack of high-resolution data and the dynamic nature of the proline-containing loop mean that the precise imide-bond conformation cannot be determined and prolyl cis-trans isomerization in the crystal cannot be ruled out. Given the preponderance of structures that have been solved by X-ray crystallography in the Protein Data Bank, this result supports the notion that prolyl isomerization in folded proteins has been underestimated among known structures. Interestingly, while the precise status of the proline residue is ambiguous, Itk SH2 crystallizes as a domain-swapped dimer. The domain-swapped structure of Itk SH2 is similar to the domain-swapped SH2 domains of Grb2 and Nck, with domain swapping occurring at the β-meander region of all three SH2 domains. Thus, for Itk SH2 structural analysis by NMR spectroscopy and X-ray crystallography revealed very different structural features: proline isomerization versus domain-swapped dimerization, respectively.
描述了白细胞介素-2酪氨酸激酶Src同源结构域（Itk SH2）的晶体结构，发现与使用核磁共振光谱对该结构域进行的研究不同，在晶体结构中不易检测到顺反脯氨酰异构化。基于Itk SH2晶体形式与Itk SH2核磁共振结构的顺式形式之间的相似性，得出结论：脯氨酰亚胺键至少部分地在晶体形式中采用顺式构象。然而，缺乏高分辨率数据以及含脯氨酸环的动态性质意味着无法确定精确的亚胺键构象，并且不能排除晶体中的脯氨酰顺反异构化。鉴于蛋白质数据库中已通过X射线晶体学解析的结构占优势，这一结果支持了在已知结构中折叠蛋白中的脯氨酰异构化被低估的观点。有趣的是，虽然脯氨酸残基的精确状态不明确，但Itk SH2以结构域交换二聚体的形式结晶。Itk SH2的结构域交换结构类似于Grb2和Nck的结构域交换SH2结构域，所有三个SH2结构域的结构域交换都发生在β-曲折区域。因此，对于Itk SH2，核磁共振光谱和X射线晶体学的结构分析分别揭示了非常不同的结构特征：脯氨酸异构化与结构域交换二聚化。
