Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis

Dunbar, Kyle L.; Chekan, Jonathan R.; Cox, Courtney; Burkhart, Brandon J.; Nair, Satish K.; Mitchell, Douglas A.

doi:10.1038/nchembio.1608

Cited by 79 publications

(172 citation statements)

References 55 publications

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“…For example, Babinger, Sterner and colleagues used SSNs to survey sequence/function space in the geranylgeranylglyceryl phosphate synthase family and identified previously unrecognized subfamilies that differ in substrate specificities from members that had been biochemically and structurally characterized [13]. Mitchell, Nair, and coworkers used SSNs to analyze sequence/function space in the YcaO superfamily of ATP-binding proteins involved in the synthesis of heterocyclic natural products [14]. van der Donk, Nair, and colleagues used SSNs to explore functional relationships among the glutaminylation domains of lantibiotic dehydratases [15].…”

Section: Sequence Similarity Network (Ssns)mentioning

confidence: 99%

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

Gerlt

Bouvier

Davidson

et al. 2015

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

717

772

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The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their “favorite” protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the “closest neighbors” of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.

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Section: Sequence Similarity Network (Ssns)mentioning

confidence: 99%

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

Gerlt

Bouvier

Davidson

et al. 2015

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

717

772

View full text Add to dashboard Cite

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“…Azol(in)e formation in TOMM systems involves the recently characterized ATP-binding YcaO family (90, 91), but neither MbnB nor MbnC bears any similarity to those enzymes, and both lack nucleotide-binding motifs. Thioamide biosynthesis is less well understood, but a YcaO family enzyme has been proposed to be responsible for thioamide biosynthesis in thioviridamide as well (88).…”

Section: Methanobactinsmentioning

confidence: 99%

Chalkophores

Kenney

Rosenzweig

2018

Annu. Rev. Biochem.

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Copper-binding metallophores, or chalkophores, play a role in microbial copper homeostasis that is analogous to that of siderophores in iron homeostasis. The best-studied chalkophores are members of the methanobactin (Mbn) family—ribosomally produced, posttranslationally modified natural products first identified as copper chelators responsible for copper uptake in methane-oxidizing bacteria. To date, Mbns have been characterized exclusively in those species, but there is genomic evidence for their production in a much wider range of bacteria. This review addresses the current state of knowledge regarding the function, biosynthesis, transport, and regulation of Mbns. While the roles of several proteins in these processes are supported by substantial genetic and biochemical evidence, key aspects of Mbn manufacture, handling, and regulation remain unclear. In addition, other natural products that have been proposed to mediate copper uptake as well as metallophores that have biologically relevant roles involving copper binding, but not copper uptake, are discussed.

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“…1,2 Previous research has demonstrated that the TOMM D domain catalyzes the ATP-dependent cyclodehydration reaction, while the TOMM C domain recognizes the peptide substrate through specific motifs within the N-terminal leader peptide and regulates D domain activity. 3–5 However, the biophysical basis for leader peptide binding and activity potentiation by the C domain has yet to be elucidated.…”

Section: Introductionmentioning

confidence: 99%

Identification of an Auxiliary Leader Peptide-Binding Protein Required for Azoline Formation in Ribosomal Natural Products

et al. 2015

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Thiazole/oxazole-modified microcins (TOMMs) are a class of posttranslationally modified peptide natural products bearing azole and azoline heterocycles. The first step in heterocycle formation is carried out by a two component cyclodehydratase comprised of an E1 ubiquitin-activating and a YcaO superfamily member. Recent studies have demonstrated that the YcaO domain is responsible for cyclodehydration while the TOMM E1 homolog is responsible for peptide recognition during azoline formation. Although all characterized TOMM biosynthetic clusters contain this canonical TOMM E1 homolog (C domain), we also identified a second, highly divergent E1 superfamily member, annotated as an Ocin-ThiF-like protein (F protein), associated with more than 300 TOMM biosynthetic clusters. Here we describe the in vitro reconstitution of a novel TOMM cyclodehydratase from such a cluster and demonstrate that this auxiliary protein is required for cyclodehydration. Using a combination of biophysical techniques we demonstrate that the F protein, rather than the C domain, is responsible for engaging the peptide substrate. The C domain instead appears to serve as a scaffolding protein, bringing the catalytic YcaO domain and the peptide binding Ocin-ThiF-like protein into proximity. Our findings provide an updated biosynthetic framework that provides a foundation for the characterization and reconstitution of approximately 25 % of bioinformatically identifiable TOMM synthetases.

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Discovery of a new ATP-binding motif involved in peptidic azoline biosynthesis

Cited by 79 publications

References 55 publications

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks

Chalkophores

Identification of an Auxiliary Leader Peptide-Binding Protein Required for Azoline Formation in Ribosomal Natural Products

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