不同序列自由基s -腺苷蛋氨酸酶功能统一的催化位点接近分析

IF 3.8 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY ACS Bio & Med Chem Au Pub Date : 2023-03-01 DOI:10.1021/acsbiomedchemau.2c00085
Timothy W. Precord, Sangeetha Ramesh, Shravan R. Dommaraju, Lonnie A. Harris, Bryce L. Kille and Douglas A. Mitchell*, 
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引用次数: 1

摘要

自由基S-腺苷甲硫氨酸(rSAM)超家族已成为发现新的酶化学的源泉,特别是在核糖体合成和翻译后修饰肽(RiPP)方面。在这里,我们报道了一份近15000个rSAM蛋白的简编,这些蛋白在RiPP生物合成中具有高置信度。尽管最近的生物信息学进展揭示了rSAM蛋白覆盖的广阔序列空间,但功能注释的重大挑战仍未解决。通过序列分析和蛋白质结构预测的结合,我们确定了一组具有功能预测能力的催化位点邻近残基,特别是在形成硫-α碳硫醚(sacionine)键的各种rSAM蛋白质中。作为一项案例研究,我们报道了稀疏链霉菌(StsB)的rSAM蛋白与MftC(分枝杆菌素生物合成)的全长相似性高于任何其他特征酶。然而,使用“催化位点接近度”对StsB与已知rSAM蛋白进行的比较分析预测,StsB将不同于MftC,而是形成阳离子键。通过质谱、靶向诱变和化学降解证实了这一预测。我们进一步使用“催化位点邻近性”分析来识别传统基因组挖掘策略无法检测到的六个新的囊肽基团。形成环乙烷的rSAM蛋白质的额外催化位点邻近性分析表明,这种方法将更广泛地应用,并增强基于传统基因组酶学原理的蛋白质功能预测,如果不是完全正确的话。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Catalytic Site Proximity Profiling for Functional Unification of Sequence-Diverse Radical S-Adenosylmethionine Enzymes

The radical S-adenosylmethionine (rSAM) superfamily has become a wellspring for discovering new enzyme chemistry, especially regarding ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, we report a compendium of nearly 15,000 rSAM proteins with high-confidence involvement in RiPP biosynthesis. While recent bioinformatics advances have unveiled the broad sequence space covered by rSAM proteins, the significant challenge of functional annotation remains unsolved. Through a combination of sequence analysis and protein structural predictions, we identified a set of catalytic site proximity residues with functional predictive power, especially among the diverse rSAM proteins that form sulfur-to-α carbon thioether (sactionine) linkages. As a case study, we report that an rSAM protein from Streptomyces sparsogenes (StsB) shares higher full-length similarity with MftC (mycofactocin biosynthesis) than any other characterized enzyme. However, a comparative analysis of StsB to known rSAM proteins using “catalytic site proximity” predicted that StsB would be distinct from MftC and instead form sactionine bonds. The prediction was confirmed by mass spectrometry, targeted mutagenesis, and chemical degradation. We further used “catalytic site proximity” analysis to identify six new sactipeptide groups undetectable by traditional genome-mining strategies. Additional catalytic site proximity profiling of cyclophane-forming rSAM proteins suggests that this approach will be more broadly applicable and enhance, if not outright correct, protein functional predictions based on traditional genomic enzymology principles.

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ACS Bio & Med Chem Au
ACS Bio & Med Chem Au 药物、生物、化学-
CiteScore
4.10
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0.00%
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0
期刊介绍: ACS Bio & Med Chem Au is a broad scope open access journal which publishes short letters comprehensive articles reviews and perspectives in all aspects of biological and medicinal chemistry. Studies providing fundamental insights or describing novel syntheses as well as clinical or other applications-based work are welcomed.This broad scope includes experimental and theoretical studies on the chemical physical mechanistic and/or structural basis of biological or cell function in all domains of life. It encompasses the fields of chemical biology synthetic biology disease biology cell biology agriculture and food natural products research nucleic acid biology neuroscience structural biology and biophysics.The journal publishes studies that pertain to a broad range of medicinal chemistry including compound design and optimization biological evaluation molecular mechanistic understanding of drug delivery and drug delivery systems imaging agents and pharmacology and translational science of both small and large bioactive molecules. Novel computational cheminformatics and structural studies for the identification (or structure-activity relationship analysis) of bioactive molecules ligands and their targets are also welcome. The journal will consider computational studies applying established computational methods but only in combination with novel and original experimental data (e.g. in cases where new compounds have been designed and tested).Also included in the scope of the journal are articles relating to infectious diseases research on pathogens host-pathogen interactions therapeutics diagnostics vaccines drug-delivery systems and other biomedical technology development pertaining to infectious diseases.
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