Industrial Enzymes National Engineering Laboratory, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, 32 Xi Qi Dao, Tianjin Airport Economic Area, Tianjin 300308 (China).
Chembiochem. 2014 Jan 24;15(2):217-22. doi: 10.1002/cbic.201300691. Epub 2013 Dec 11.
Wild-type meso-diaminopimelate dehydrogenase (DAPDH) is usually specific to the native substrate, meso-2,6-diaminopimelate. Recently, a DAPDH from Symbiobacterium thermophilum (StDAPDH) was found to exhibit expanded substrate specificity. As such, its crystal structures in apo form and in complex with NADP(+) and both NADPH and meso-DAP were investigated to reveal the structural basis of its unique catalytic properties. Structural analysis results show that StDAPDH should prefer an ordered kinetic catalytic mechanism. A second substrate entrance tunnel with Met152 at its bottleneck was found, through which pyruvate/D-alanine might bind and enter the catalytic cavity, providing some structural insights into its high activity toward pyruvate. The side chain of Met152 might interact with Asp92 and Asn253, thus affecting the domain motion and catalysis. These results offer useful information for understanding the unique catalytic properties of StDAPDH and guiding further engineering of this enzyme.
野生型中-二氨基庚二酸脱氢酶（DAPDH）通常对天然底物中-2,6-二氨基庚二酸具有特异性。最近，从嗜热共生菌（Symbiobacterium thermophilum）中发现了一种 DAPDH（StDAPDH），它表现出扩展的底物特异性。因此，研究了其apo 形式以及与 NADP(+)和 NADPH 与 meso-DAP 的复合物的晶体结构，以揭示其独特催化特性的结构基础。结构分析结果表明，StDAPDH 应该倾向于有序的动力学催化机制。发现了第二个底物入口隧道，其瓶颈处是 Met152，通过该隧道，丙酮酸/D-丙氨酸可能结合并进入催化腔，为其对丙酮酸的高活性提供了一些结构见解。Met152 的侧链可能与 Asp92 和 Asn253 相互作用，从而影响结构域运动和催化。这些结果为理解 StDAPDH 的独特催化特性提供了有用的信息，并指导了该酶的进一步工程改造。
