An ancient metalloenzyme evolves through metal preference modulation.
An ancient metalloenzyme evolves through metal preference modulation.
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DOI：
10.1038/s41559-023-02012-0
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发表时间：
2023-05
影响因子：
16.8
通讯作者：
中科院分区：
文献类型：
--
作者：
进化创造了蛋白质的功能多样性，蛋白质是所有生物系统的基本组成部分。然而，缺乏对整个生命树中的天然蛋白质进行采样并在单一实验系统中进行评估的研究。几乎一半的酶需要金属，而金属蛋白往往最佳地利用特定金属辅因子的物理化学性质。生命必须适应金属生物利用度的变化，包括从缺氧到有氧地球的过渡过程中或病原体暴露于营养免疫的过程中。这些变化可能会挑战金属酶维持活性的能力，推测会推动它们的进化。在这里，我们研究了铁/锰超氧化物歧化酶（SodFM）家族的活性氧清除剂的自然多样性内的金属偏好进化。我们确定并实验验证了在确定金属偏好中具有保守作用的残基，当与对蛋白质进化历史的理解相结合时，改进了对本文定义的五个SodFM亚家族的金属利用率的预测。通过结合遗传学，生物化学和结构生物学，我们证明，SodFM金属利用可以通过滑动沿着完美的锰和铁特异性之间的尺度进行进化微调。在生命的历史中，SodFM金属偏好已经在不同的进化和生态背景下被调制了多个独立的时间，并且可以在短的进化时间内改变。铁/锰超氧化物歧化酶是一类具有清除活性氧功能的金属酶。在这里，作者使用遗传学，生物化学和结构生物学，以显示如何不同的金属偏好铁和锰已调制整个铁/锰超氧化物歧化酶的演变。
Evolution creates functional diversity of proteins, the essential building blocks of all biological systems. However, studies of natural proteins sampled across the tree of life and evaluated in a single experimental system are lacking. Almost half of enzymes require metals, and metalloproteins tend to optimally utilize the physicochemical properties of a specific metal co-factor. Life must adapt to changes in metal bioavailability, including those during the transition from anoxic to oxic Earth or pathogens’ exposure to nutritional immunity. These changes can challenge the ability of metalloenzymes to maintain activity, presumptively driving their evolution. Here we studied metal-preference evolution within the natural diversity of the iron/manganese superoxide dismutase (SodFM) family of reactive oxygen species scavengers. We identified and experimentally verified residues with conserved roles in determining metal preference that, when combined with an understanding of the protein’s evolutionary history, improved prediction of metal utilization across the five SodFM subfamilies defined herein. By combining phylogenetics, biochemistry and structural biology, we demonstrate that SodFM metal utilization can be evolutionarily fine tuned by sliding along a scale between perfect manganese and iron specificities. Over the history of life, SodFM metal preference has been modulated multiple independent times within different evolutionary and ecological contexts, and can be changed within short evolutionary timeframes. The iron/manganese superoxide dismutases constitute a family of metalloenzymes that function as scavengers of reactive oxygen species. Here the authors use phylogenetics, biochemistry and structural biology to show how differential metal preference for Fe and Mn has been modulated throughout iron/manganese superoxide dismutases evolution.
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影响因子：
16.6
作者：
Dean P;Sendra KM;Williams TA;Watson AK;Major P;Nakjang S;Kozhevnikova E;Goldberg AV;Kunji ERS;Hirt RP;Embley TM
通讯作者：
Embley TM
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
3
作者：
Andreini, Claudia;Bertini, Ivano;Thornton, Janet M.
通讯作者：
Thornton, Janet M.
DOI：
10.1046/j.1432-1327.1998.2510795.x
发表时间：
1998-02-01
期刊：
EUROPEAN JOURNAL OF BIOCHEMISTRY
影响因子：
--
作者：
Bunting, K;Cooper, JB;Young, D
通讯作者：
Young, D
影响因子：
10.7
作者：
Hoang DT;Chernomor O;von Haeseler A;Minh BQ;Vinh LS
通讯作者：
Vinh LS