Jeyakanthan Jeyaraman, Kanaujia Shankar Prasad, Nishida Yuya, Nakagawa Noriko, Praveen Surendran, Shinkai Akeo, Kuramitsu Seiki, Yokoyama Shigeyuki, Sekar Kanagaraj
Life Science Group, National Synchrotron Radiation Research Center, 101 Hsin-Ann Road, Hsinchu Science Park, Hsinchu 30076, Taiwan.
Acta Crystallogr D Biol Crystallogr. 2010 Feb;66(Pt 2):116-24. doi: 10.1107/S0907444909047064. Epub 2010 Jan 22.
Asymmetric diadenosine tetraphosphate (Ap(4)A) hydrolases degrade the metabolite Ap(4)A back into ATP and AMP. The three-dimensional crystal structure of Ap(4)A hydrolase (16 kDa) from Aquifex aeolicus has been determined in free and ATP-bound forms at 1.8 and 1.95 A resolution, respectively. The overall three-dimensional crystal structure of the enzyme shows an alphabetaalpha-sandwich architecture with a characteristic loop adjacent to the catalytic site of the protein molecule. The ATP molecule is bound in the primary active site and the adenine moiety of the nucleotide binds in a ring-stacking arrangement equivalent to that observed in the X-ray structure of Ap(4)A hydrolase from Caenorhabditis elegans. Binding of ATP in the active site induces local conformational changes which may have important implications in the mechanism of substrate recognition in this class of enzymes. Furthermore, two invariant water molecules have been identified and their possible structural and/or functional roles are discussed. In addition, modelling of the substrate molecule at the primary active site of the enzyme suggests a possible path for entry and/or exit of the substrate and/or product molecule.
不对称二腺苷四磷酸（Ap(4)A）水解酶将代谢产物Ap(4)A降解回ATP和AMP。嗜热栖热菌中16 kDa的Ap(4)A水解酶的三维晶体结构已分别在1.8 Å和1.95 Å分辨率下以游离形式和ATP结合形式确定。该酶的整体三维晶体结构显示出一种αβ-α三明治结构，在蛋白质分子的催化位点附近有一个特征性环。ATP分子结合在主要活性位点，核苷酸的腺嘌呤部分以一种与秀丽隐杆线虫Ap(4)A水解酶的X射线结构中观察到的环堆积排列方式结合。ATP在活性位点的结合诱导了局部构象变化，这可能对这类酶的底物识别机制具有重要意义。此外，已鉴定出两个不变水分子，并讨论了它们可能的结构和/或功能作用。此外，对酶主要活性位点的底物分子建模表明了底物和/或产物分子进入和/或离开的可能途径。
