反刍硒单胞菌乳酸脱氢酶的生化、结构和动力学特征提供了关于乳酸和苹果酸脱氢酶超家族中完全变构调节获得之前的中间进化步骤的信息。

IF 3 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Quentin Bertrand , Sandrine Coquille , Antonio Iorio , Fabio Sterpone , Dominique Madern
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引用次数: 0

摘要

在这项工作中,我们研究了反刍硒单胞菌(S.rum)的乳酸脱氢酶(LDH),这是一种在关键氨基酸位置与经典变构LDH不同的酶。这种酶的野生型(Wt)将丙酮酸盐识别为所有的LDH。然而,在活性位点环(I85R)中引入单点突变使S.Rum LDH能够将草酰乙酸底物识别为典型的苹果酸脱氢酶(MalDH),同时保持LDH的同源激活。我们报道了Wt和I85RLDH突变体的三级结构。Wt S.rum酶结构结合NADH和丙二酸,同时也类似于典型LDH的典型紧密R-活性状态。具有I85R的突变体的结构在Apo状态(没有配体)下被溶解,并且没有显示出大的构象重组,例如在Apo态下用经典变构LDH观察到的构象重组。这是由于S.rum LDH典型的局部结构特征阻止了大规模构象重组。还使用分子动力学模拟研究了S.rum LDH,探测活性位点的特定局部变形,从而使S.rum乳酸脱氢酶能够对T无活性状态进行采样。我们提出,相对于LDH/MalDH超家族,S.rum酶具有特定的结构和动力学方式来确保同源激活。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases

Biochemical, structural and dynamical characterizations of the lactate dehydrogenase from Selenomonas ruminantium provide information about an intermediate evolutionary step prior to complete allosteric regulation acquisition in the super family of lactate and malate dehydrogenases

In this work, we investigated the lactate dehydrogenase (LDH) from Selenomonas ruminantium (S. rum), an enzyme that differs at key amino acid positions from canonical allosteric LDHs. The wild type (Wt) of this enzyme recognises pyuvate as all LDHs. However, introducing a single point mutation in the active site loop (I85R) allows S. Rum LDH to recognize the oxaloacetate substrate as a typical malate dehydrogenase (MalDH), whilst maintaining homotropic activation as an LDH. We report the tertiary structure of the Wt and I85R LDH mutant.

The Wt S. rum enzyme structure binds NADH and malonate, whilst also resembling the typical compact R-active state of canonical LDHs. The structure of the mutant with I85R was solved in the Apo State (without ligand), and shows no large conformational reorganization such as that observed with canonical allosteric LDHs in Apo state. This is due to a local structural feature typical of S. rum LDH that prevents large-scale conformational reorganization. The S. rum LDH was also studied using Molecular Dynamics simulations, probing specific local deformations of the active site that allow the S. rum LDH to sample the T-inactive state. We propose that, with respect to the LDH/MalDH superfamily, the S. rum enzyme possesses a specific structural and dynamical way to ensure homotropic activation.

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来源期刊
Journal of structural biology
Journal of structural biology 生物-生化与分子生物学
CiteScore
6.30
自引率
3.30%
发文量
88
审稿时长
65 days
期刊介绍: Journal of Structural Biology (JSB) has an open access mirror journal, the Journal of Structural Biology: X (JSBX), sharing the same aims and scope, editorial team, submission system and rigorous peer review. Since both journals share the same editorial system, you may submit your manuscript via either journal homepage. You will be prompted during submission (and revision) to choose in which to publish your article. The editors and reviewers are not aware of the choice you made until the article has been published online. JSB and JSBX publish papers dealing with the structural analysis of living material at every level of organization by all methods that lead to an understanding of biological function in terms of molecular and supermolecular structure. Techniques covered include: • Light microscopy including confocal microscopy • All types of electron microscopy • X-ray diffraction • Nuclear magnetic resonance • Scanning force microscopy, scanning probe microscopy, and tunneling microscopy • Digital image processing • Computational insights into structure
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