Chemical Logic of Peptide Branching by Iterative Nonlinear Nonribosomal Peptide Synthetases.

IF 2.9 3区 生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY
Biochemistry Biochemistry Pub Date : 2025-02-04 Epub Date: 2025-01-23 DOI:10.1021/acs.biochem.4c00749
Jinping Yang, Adam Balutowski, Megan Trivedi, Timothy A Wencewicz
{"title":"Chemical Logic of Peptide Branching by Iterative Nonlinear Nonribosomal Peptide Synthetases.","authors":"Jinping Yang, Adam Balutowski, Megan Trivedi, Timothy A Wencewicz","doi":"10.1021/acs.biochem.4c00749","DOIUrl":null,"url":null,"abstract":"<p><p>Branch-point syntheses in nonribosomal peptide assembly are rare but useful strategies to generate tripodal peptides with advantageous hexadentate iron-chelating capabilities, as seen in siderophores. However, the chemical logic underlying the peptide branching by nonribosomal peptide synthetase (NRPS) often remains complex and elusive. Here, we review the common strategies for the biosynthesis of branched nonribosomal peptides (NRPs) and present our biochemical investigation on the NRPS-catalyzed assembly of fimsbactin A, a branched mixed-ligand siderophore produced by the human pathogenic strain <i>Acinetobacter baumannii</i>. We untangled the unusual branching mechanism of fimsbactin A biosynthesis through a combination of bioinformatics, site-directed mutagenesis, <i>in vitro</i> reconstitution, molecular modeling, and molecular dynamics simulation. Our findings clarify the roles of the fimsbactin NRPS enzymes, uncovering catalytically redundant domains and identifying the multifunctional nature of the FbsF cyclization (Cy) domain. We demonstrate the dynamic interplay between l-serine and 2,3-dihydroxybenzoic acid derived dipeptides, partitioning between amide and ester forms via a 1,2-<i>N</i>-to-<i>O</i>-acyl shift orchestrated by the noncanonical, multichannel FbsF Cy domain. The branching event occurs in a secondary condensation event facilitated by this Cy domain with two dipeptidyl intermediates, which generates a branched tetrapeptide thioester. Finally, the terminal condensation domain of FbsG recruits a soluble nucleophile to release the final product. This study advances our understanding of the intricate biosynthetic pathways and chemical logic employed by NRPSs, shedding light on the mechanisms underlying the synthesis of complex branched peptides.</p>","PeriodicalId":28,"journal":{"name":"Biochemistry Biochemistry","volume":" ","pages":"719-734"},"PeriodicalIF":2.9000,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Biochemistry Biochemistry","FirstCategoryId":"1","ListUrlMain":"https://doi.org/10.1021/acs.biochem.4c00749","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/1/23 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Branch-point syntheses in nonribosomal peptide assembly are rare but useful strategies to generate tripodal peptides with advantageous hexadentate iron-chelating capabilities, as seen in siderophores. However, the chemical logic underlying the peptide branching by nonribosomal peptide synthetase (NRPS) often remains complex and elusive. Here, we review the common strategies for the biosynthesis of branched nonribosomal peptides (NRPs) and present our biochemical investigation on the NRPS-catalyzed assembly of fimsbactin A, a branched mixed-ligand siderophore produced by the human pathogenic strain Acinetobacter baumannii. We untangled the unusual branching mechanism of fimsbactin A biosynthesis through a combination of bioinformatics, site-directed mutagenesis, in vitro reconstitution, molecular modeling, and molecular dynamics simulation. Our findings clarify the roles of the fimsbactin NRPS enzymes, uncovering catalytically redundant domains and identifying the multifunctional nature of the FbsF cyclization (Cy) domain. We demonstrate the dynamic interplay between l-serine and 2,3-dihydroxybenzoic acid derived dipeptides, partitioning between amide and ester forms via a 1,2-N-to-O-acyl shift orchestrated by the noncanonical, multichannel FbsF Cy domain. The branching event occurs in a secondary condensation event facilitated by this Cy domain with two dipeptidyl intermediates, which generates a branched tetrapeptide thioester. Finally, the terminal condensation domain of FbsG recruits a soluble nucleophile to release the final product. This study advances our understanding of the intricate biosynthetic pathways and chemical logic employed by NRPSs, shedding light on the mechanisms underlying the synthesis of complex branched peptides.

迭代非线性非核糖体多肽合成酶分支的化学逻辑。
分支点合成在非核糖体肽组装是罕见的,但有用的策略,以产生具有优势的六齿铁螯合能力的三足肽,如在铁载体中所见。然而,由非核糖体肽合成酶(NRPS)形成肽分支的化学逻辑往往仍然是复杂和难以捉摸的。在这里,我们回顾了分枝非核糖体肽(nrp)生物合成的常见策略,并介绍了我们对nrp催化的fimsbactin A组装的生化研究,fimsbactin A是由人类致病菌株鲍曼不动杆菌产生的一种分枝混合配体铁载体。我们通过结合生物信息学、定点诱变、体外重构、分子建模和分子动力学模拟,解开了fimsbactin A生物合成的不同寻常的分支机制。我们的研究结果阐明了fimsbactin NRPS酶的作用,揭示了催化冗余结构域,并确定了FbsF环化(Cy)结构域的多功能性质。我们证明了l-丝氨酸和2,3-二羟基苯甲酸衍生的二肽之间的动态相互作用,酰胺和酯形式之间的分配通过非规范的多通道FbsF Cy结构域协调的1,2- n - o-酰基转移。支化反应发生在Cy结构域与两个二肽基中间体的二次缩合反应中,生成支化的四肽硫酯。最后,FbsG的末端缩合域吸收可溶性亲核试剂释放最终产物。这项研究促进了我们对NRPSs复杂的生物合成途径和化学逻辑的理解,揭示了复杂支链肽合成的机制。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Biochemistry Biochemistry
Biochemistry Biochemistry 生物-生化与分子生物学
CiteScore
5.50
自引率
3.40%
发文量
336
审稿时长
1-2 weeks
期刊介绍: Biochemistry provides an international forum for publishing exceptional, rigorous, high-impact research across all of biological chemistry. This broad scope includes studies on the chemical, physical, mechanistic, and/or structural basis of biological or cell function, and encompasses the fields of chemical biology, synthetic biology, disease biology, cell biology, nucleic acid biology, neuroscience, structural biology, and biophysics. In addition to traditional Research Articles, Biochemistry also publishes Communications, Viewpoints, and Perspectives, as well as From the Bench articles that report new methods of particular interest to the biological chemistry community.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信