Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle.
Identifying structural and dynamic changes during the Biliverdin Reductase B catalytic cycle.
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DOI：
10.3389/fmolb.2023.1244587
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发表时间：
2023
影响因子：
5
通讯作者：
中科院分区：
文献类型：
--
作者：
胆绿素还原酶B(BLVRB)是一种NADPH依赖的还原酶，可催化多种底物的还原，因此被认为是细胞内重要的氧化还原调节因子。在这项研究中，我们试图解决是否结构和动力学变化都发生在催化循环的不同中间体之间，以及这些变化是否仅限于酶的活性部位或整个酶。通过X射线结晶学，我们首次确定了apo BLVRB的结构，揭示了与全息结构相比的微妙的全局变化，并确定了失去了一个关键的氢键，该氢键“夹住”了辅酶上的R78-环。酰胺和C-α化学位移微扰被用来识别中间体之间的环境和二级结构变化，与底物相互作用相比，辅酶结合时观察到的全球变化更远。核磁共振弛豫速率测量为了解BLVRB在催化循环中的动态行为提供了深入的了解。具体地说，在辅酶结合时变得有序的固有动态R78-环在催化循环中持续，而类似的区域经历动态交换。然而，在催化循环中，动态交换过程被发现是不同的，有几组残基表现出相似的动态响应。最后，局部和远端的结构和动态变化都发生在BLVRB内，这些变化完全依赖于辅酶的氧化状态。因此，通过这里的综合分析，本研究揭示了BLVRB在其催化循环中的结构和动态变化，这些变化不是简单地归类到活性部位，而是在整个酶中变构耦合。
Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that catalyzes the reduction of multiple substrates and is therefore considered a critical cellular redox regulator. In this study, we sought to address whether both structural and dynamics changes occur between different intermediates of the catalytic cycle and whether these were relegated to just the active site or the entirety of the enzyme. Through X-ray crystallography, we determined the apo BLVRB structure for the first time, revealing subtle global changes compared to the holo structure and identifying the loss of a critical hydrogen bond that “clamps” the R78-loop over the coenzyme. Amide and Cα chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, with more distant global changes observed upon coenzyme binding compared to substrate interactions. NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB during the catalytic cycle. Specifically, the inherently dynamic R78-loop that becomes ordered upon coenzyme binding persists through the catalytic cycle while similar regions experience dynamic exchange. However, the dynamic exchange processes were found to differ through the catalytic cycle with several groups of residues exhibiting similar dynamic responses. Finally, both local and distal structural and dynamic changes occur within BLVRB that are dependent solely on the oxidative state of the coenzyme. Thus, through a comprehensive analysis here, this study revealed structural and dynamic alterations in BLVRB through its catalytic cycle that are not simply relegated to the active site, but instead, are allosterically coupled throughout the enzyme.
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影响因子：
5.7
作者：
Huan L;Bao C;Chen D;Li Y;Lian J;Ding J;Huang S;Liang L;He X
通讯作者：
He X
DOI：
10.1016/j.str.2018.01.015
发表时间：
2018-03-06
期刊：
Structure (London, England : 1993)
影响因子：
--
作者：
Narayanan C;Bernard DN;Bafna K;Gagné D;Chennubhotla CS;Doucet N;Agarwal PK
通讯作者：
Agarwal PK
影响因子：
4.7
作者：
Ramberg H;Richardsen E;de Souza GA;Rakaee M;Stensland ME;Braadland PR;Nygård S;Ögren O;Guldvik IJ;Berge V;Svindland A;Taskén KA;Andersen S
通讯作者：
Andersen S
影响因子：
15
作者：
Millet, O;Loria, JP;Palmer, AG
通讯作者：
Palmer, AG
影响因子：
4.1
作者：
Cunningham, O;Gore, MG;Mantle, TJ
通讯作者：
Mantle, TJ