A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums
A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums
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DOI：
10.3390/ijms131012994
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发表时间：
2012-10-01
影响因子：
5.6
通讯作者：
Gauld, James W.
中科院分区：
文献类型：
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作者：
Ion, Bogdan F.;Bushnell, Eric A. C.;Gauld, James W.
鸟氨酸环脱氨酶（OCD）是一种NAD（+）依赖性脱氨酶，发现于细菌物种，如恶臭假单胞菌。重要的是，它催化氨基酸L-鸟氨酸直接转化为L-脯氨酸。利用分子动力学（MD）和混合量子力学/分子力学（QM/MM）方法，在ONIOM形式主义，强迫症的催化机制进行了研究。速率限制步骤被计算为整个机制的初始步骤：氢化物从L-鸟氨酸的C-alpha-H基团转移到NAD（+）辅因子，伴随着形成C-alpha= NH 2+席夫碱，势垒为90.6 kJ mol（-1）。重要的是，在MD模拟过程中，在活性位点内没有观察到水，所述活性位点被适当地定位以水解C-alpha= NH 2+中间体以形成相应的羰基。相反，反应通过非水解机制进行，该机制涉及δ-胺在C-α-位的直接亲核攻击。然后裂解并失去α-NH 2基团，得到δ（1）-吡咯啉-2-羧酸酯，随后将其还原为L-脯氨酸。
Ornithine cyclodeaminase (OCD) is an NAD(+)-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine's C-alpha-H group to the NAD(+) cofactor with concomitant formation of a C-alpha=NH2+ Schiff base with a barrier of 90.6 kJ mol(-1). Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the C-alpha=NH2+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the delta-amine at the C-alpha-position. This is then followed by cleavage and loss of the alpha-NH2 group to give the Delta(1)-pyrroline-2-carboxylate that is subsequently reduced to L-proline.