Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.
Active-site protein dynamics and solvent accessibility in native Achromobacter cycloclastes copper nitrite reductase.
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天然achromobacter环形细胞的活性位点蛋白动力学和溶剂可及性可铜亚硝酸盐还原酶。
DOI：
10.1107/s2052252517007527
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发表时间：
2017-07-01
期刊：
影响因子：
3.9
通讯作者：
Strange RW
中科院分区：
文献类型：
--
作者：
Sen K;Horrell S;Kekilli D;Yong CW;Keal TW;Atakisi H;Moreau DW;Thorne RE;Hough MA;Strange RW
从一个晶体的亚硝酸铜还原酶在升高的低温下，与分子动力学模拟一起获得的多个结构，揭示了催化重要的蛋白质和溶剂动力学的活性位点。微生物亚硝酸盐还原酶是一种硝化酶，是全球氮循环的主要成分。从一个晶体（MSOX数据）的亚硝酸铜还原酶在240 K，连同分子动力学模拟测量的多个结构，揭示了蛋白质动力学在2型铜网站，是显着的催化性能和进出的溶剂或配体的活性位点。 分子动力学模拟进行了使用不同的质子化状态的关键催化残基（AspCAT和HisCAT）参与这种酶的亚硝酸盐还原机制。两者合计，晶体结构和模拟表明，AspCAT的质子化状态强烈影响的活性位点溶剂的可及性，而活性位点的“封端残基”（IleCAT），配体结合的决定因素的动力学，受到温度和AspCAT的质子化状态的影响。一个以前未观察到的构象IleCAT被认为是在高温系列相比，100 K的结构。 DFT计算还表明，在MSOX系列的活性位点的结合水配体的损失是一致的减少2型铜原子。
Multiple structures obtained from one crystal of copper nitrite reductase at elevated cryogenic temperature, together with molecular-dynamics simulations, reveal catalyically important protein and solvent dynamics at the active site. Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCAT and HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCAT protonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site ‘capping residue’ (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCAT is seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.