About

Satish K Nair is a professor in the Department of Biochemistry at the University of Illinois, with additional affiliations including the Center for Biophysics and Quantitative Biology, the School of Molecular and Cellular Biology, the Materials Research Lab, and the Carl R. Woese Institute for Genomic Biology. His research focuses on understanding the biosynthesis and application of bacterial natural products through biochemical, microbiological, and biophysical techniques, particularly X-ray crystallography. His work includes studying how bacteria produce small molecules that regulate intra-species behavior or combat competing species, with implications for developing therapeutic agents against pathogens. Nair's research encompasses the biosynthesis of ribosomally synthesized peptide antibiotics such as lantibiotics and cyanobactins, as well as phosphonate biosynthesis and engineering. He investigates bacterial inter- and intracellular communication mechanisms, including quorum sensing and diffusible signal factors, aiming to identify targets for therapeutic intervention. His educational background includes a B.S. from Brown University, a Ph.D. from the University of Pennsylvania, and postdoctoral work at Rockefeller University. His contributions advance understanding of natural product biosynthesis, enzyme mechanisms, and bacterial signaling pathways.

Research topics

• Biology
• Computer Science
• Computational biology
• Biochemistry
• Data science
• Engineering
• Bioinformatics
• Genetics
• Combinatorial chemistry
• Chemistry

Selected publications

• Discovery of the Phosphonate Flavophos Produced by <i>Burkholderia</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-16 · 1 citations

  articleOpen access

  Abstract Phosphonate natural products have proven value to society as antibiotics and herbicides. They inhibit a range of enzyme targets usually by mimicking the enzyme substrates. In this study, we investigate a family of phosphonate biosynthetic gene clusters (BGCs) found in Burkholderia . Heterologous expression in Escherichia coli resulted in production of an antimicrobial compound. Spectroscopic characterization and chemical synthesis assigned its structure as 2,4-dioxopentylphosphonic acid. One of the biosynthetic enzymes is a member of the domain of unknown function (DUF) 849 family with homology to β-keto acid cleavage enzymes (BKACEs). In vitro characterization shows that this enzyme catalyzes chemistry that is divergent from previously characterized BKACEs. The observed catalytic activity is explained by a series of co-crystal structures with substrates and intermediates. The BGC also contains a gene encoding lumazine synthase (LS), an essential enzyme in flavin biosynthesis. Biochemical experiments revealed that 2,4-dioxopentylphosphonic acid inhibits LS. In addition, expression of the LS encoded in the BGC, or LS orthologs from a range of organisms, in E. coli conferred resistance to the new phosphonate, which we therefore name flavophos.

  PublisherOA PDFDOI

• Enhancing Enzymatic Bioconjugation Efficiency via Computer-Based Installation of a Substrate Recruitment Domain

  Bioconjugate Chemistry · 2026-03-17

  articleOpen access

  Enzyme mediated bioconjugation provides a method for easy and rapid formation of protein-protein and protein-small molecule conjugates under mild conditions. Promiscuous enzymes are of particular interest because they can catalyze conjugation reactions on a broad set of substrates. However, this promiscuity carries the risk of undesirable off-target modifications. To mitigate this effect, we used computational design to install a substrate recruitment domain (SRD) onto the promiscuous enzyme, tyrosinase. The redesigned tyrosinase, called design42 (D42), preferentially modifies tyrosine residues adjacent to a 6-amino acid recognition motif/sequence (RS) that is bound by the SRD. Incorporation of the recognition sequence along with a neighboring tyrosine in peptides or proteins allows for rapid D42-mediated conversion of the tyrosine to an orthoquinone, which can be selectively modified with a variety of nucleophiles. We demonstrate the utility of our design system by rapidly installing cytotoxic molecules on a monoclonal antibody.

  PublisherDOI

• Discovery of the Phosphonate Flavophos Produced by <i>Burkholderia</i>

  Journal of the American Chemical Society · 2026-04-27 · 1 citations

  articleCorresponding

  Phosphonate natural products have proven value to society as antibiotics and herbicides. They inhibit a range of enzyme targets usually by mimicking the enzyme substrates. In this study, we investigate a family of phosphonate biosynthetic gene clusters (BGCs) found in Burkholderia. Heterologous expression in Escherichia coli resulted in production of an antimicrobial compound. Spectroscopic characterization and chemical synthesis assigned its structure as 2,4-dioxopentylphosphonic acid. One of the biosynthetic enzymes is a member of the domain of unknown function (DUF) 849 family with homology to β-keto acid cleavage enzymes (BKACEs). In vitro characterization shows that this enzyme catalyzes chemistry that is divergent from previously characterized BKACEs. The observed catalytic activity is explained by a series of cocrystal structures with substrates and intermediates. The BGC also contains a gene encoding lumazine synthase (LS), an essential enzyme in flavin biosynthesis. Biochemical experiments revealed that 2,4-dioxopentylphosphonic acid inhibits LS. In addition, expression of the LS encoded in the BGC, or LS orthologs from a range of organisms, in E. coli conferred resistance to the new phosphonate, which we therefore name flavophos.

  PublisherDOI

• Genetic and biochemical characterization of a radical SAM enzyme required for post-translational glutamine methylation of methyl-coenzyme M reductase

  mBio · 2025-01-08 · 5 citations

  articleOpen access

  ABSTRACT Methyl-coenzyme M reductase (MCR), the key catalyst in the anoxic production and consumption of methane, contains an unusual 2-methylglutamine residue within its active site. In vitro data show that a B12-dependent radical SAM (rSAM) enzyme, designated MgmA, is responsible for this post-translational modification (PTM). Here, we show that two different MgmA homologs are able to methylate MCR in vivo when expressed in Methanosarcina acetivorans , an organism that does not normally possess this PTM. M. acetivorans strains expressing MgmA showed small, but significant, reductions in growth rates and yields on methylotrophic substrates. Structural characterization of the Ni(II) form of Gln-methylated M. acetivorans MCR revealed no significant differences in the protein fold between the modified and unmodified enzyme; however, the purified enzyme contained the heterodisulfide reaction product, as opposed to the free cofactors found in eight prior M. acetivorans MCR structures, suggesting that substrate/product binding is altered in the modified enzyme. Structural characterization of MgmA revealed a fold similar to other B12-dependent rSAMs, with a wide active site cleft capable of binding an McrA peptide in an extended, linear conformation. IMPORTANCE Methane plays a key role in the global carbon cycle and is an important driver of climate change. Because MCR is responsible for nearly all biological methane production and most anoxic methane consumption, it plays a major role in setting the atmospheric levels of this important greenhouse gas. Thus, a detailed understanding of this enzyme is critical for the development of methane mitigation strategies.

  PublisherDOI

• Combatting virulent gut bacteria by inhibiting the biosynthesis of a two-component lanthipeptide toxin

  Nature Communications · 2025-07-28 · 3 citations

  articleOpen access

  The enterococcal cytolysin is a toxic, two-component ribosomally synthesized and post-translationally modified peptide (RiPP) produced by pathogenic Enterococcus faecalis. Cytolysin-producing (C+) E. faecalis resides in the gut microbiome in a commensal role, but results in negative clinical outcomes in alcoholic hepatitis patients. To potentially combat cytolysin virulence, we report inhibitors of its maturation. An extracellular serine protease CylA that is essential for toxin activation is chosen as target. A series of α-aminopeptide boronic acids are designed and synthesized that block cytolysin maturation at low micromolar to nanomolar concentrations in vitro. A crystal structure of CylA provides insights into substrate recognition, autocatalytic activation of the enzyme, and toxin maturation. The inhibitors block hemolytic activity, reduce the amount of cytolysin, and attenuate expression of the cytolysin biosynthetic gene cluster without impeding cell growth. These studies provide a potential route to the development of treatments for cytolysin-induced disease states.

  PublisherOA PDFDOI

• <i>Bacillus subtilis</i> Utilizes Decarboxylated <i>S</i>-Adenosylmethionine for the Biosynthesis of Tandem Aminopropylated Microcin C, a Potent Inhibitor of Bacterial Aspartyl-tRNA Synthetase

  Journal of the American Chemical Society · 2025-03-31 · 4 citations

  article

  The biosynthetic pathways of natural products involve unusual biochemical reactions catalyzed by unique enzymes. Aminopropylation, although apparently simple, is an extremely rare modification outside polyamine biosynthesis. The canonical pathway used in the biosynthesis of peptide-adenylate antibiotic microcin C of E. coli (Eco-McC) entails alkylation by the S-adenosyl-methionine-derived 3-amino-3-carboxypropyl group of the adenylate moiety and subsequent decarboxylation to yield the bioactive aminopropylated compound. Here, we report the structure and biosynthesis of a new member of the microcin C family of antibiotics, Bsu-McC, produced by Bacillus subtilis MG27, which employs an alternative aminopropylation pathway. Like Eco-McC, Bsu-McC consists of a peptide moiety that facilitates prodrug import into susceptible bacteria and a warhead, a nonhydrolyzable modified isoasparaginyl-adenylate, which, when released into the cytoplasm, binds aspartyl-tRNA synthetase (AspRS) inhibiting translation. In contrast to the Eco-McC, whose warhead carries a single aminopropyl group attached to the phosphate moiety of isoasparaginyl-adenylate, the warhead of Bsu-McC is decorated with a tandem of two aminopropyl groups. Our in silico docking of the Bsu-McC warhead to the AspRS-tRNA complex suggests that two aminopropyl groups form extended interactions with the enzyme and tRNA, stabilizing the enzyme–inhibitor complex. We show that tandem aminopropylation results in a 32-fold increase in the biological activity of peptidyl-adenylate. We also show that B. subtilis adopted an alternative pathway for aminopropylation in which two homologous 3-aminopropyltransferases utilize decarboxylated S-adenosylmethionine as a substrate. Additionally, Bsu-McC biosynthesis alters the social behavior of the B. subtilis producer strain, resulting in a sharp decrease in their ability to form biofilms.

  PublisherDOI

• The redox landscape of pyruvate:ferredoxin oxidoreductases reveals often conserved Fe–S cluster potentials

  Journal of Biological Chemistry · 2025-06-16 · 2 citations

  articleOpen access

  Here, we investigate the thermodynamic driving force of internal electron transfer of pyruvate:ferredoxin oxidoreductases (PFORs), by comparing the redox properties of a series of PFORs from Chlorobaculum tepidum, Magnetococcus marinus, Methanosarcina acetivorans, as well as revisiting the single historical precedent, the enzyme from Desulfovibrio africanus. These enzymes require a thiamine pyrophosphate cofactor, three [4Fe-4S] clusters, and CoA for activity and are found within anaerobic organisms that utilize the reverse tricarboxylic acid cycle, or other reductive pathways, performing carbon dioxide reduction and pyruvate synthesis. Yet, PFOR is often invoked as an oxidative enzyme responsible for generating reducing equivalents in the form of the redox carrier ferredoxin. Previous efforts to understand the mechanism of PFOR have relied upon a prior report of the iron-sulfur redox potentials derived from an incomplete redox titration. Here, we use direct protein film electrochemistry to provide a side-by-comparison of four PFOR enzymes, providing a new assessment of the iron-sulfur cluster redox potentials. As the Methanosarcina acetivorans PFOR is comprised of multiple polypeptides, our investigation of the recombinant PorD subunit allows us to construct a model, where the revised redox potentials are mapped to specific iron-sulfur clusters.

  PublisherOA PDFDOI

• Structure-based discovery and definition of RiPP recognition elements

  mSystems · 2025-11-18 · 2 citations

  articleOpen access

  Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of natural products with wide-ranging structural and functional diversity. Central to many RiPP biosynthetic pathways is the RiPP Recognition Element (RRE), a structurally conserved peptide-binding domain that enables class-independent genome mining. Bioinformatic tools, such as RRE-Finder, have leveraged this domain to identify novel RiPPs, but accuracy has been limited by high false-positive rates. To improve accuracy, we assessed whether structure-based searching of the AlphaFold database with the rapid tertiary structure alignment tool Foldseek could reduce false-positive rates and identify previously unretrievable, sequence-divergent RREs. We used these divergent RREs to build 11 new Foldseek-derived Hidden Markov Models (HMMs) and refined existing models through improved seed alignments, domain excision, bit score thresholds, and Pfam filters. Improved precision mode HMMs retrieved nearly twice as many RREs from the UniProt database as the original models, including novel domain fusions. In total, the updated workflow identified >90,000 high-confidence RREs. To further characterize these RREs and assess their functional relevance, we used a combined bioinformatic and AlphaFold 3 approach to predict over 8,000 RRE-peptide complexes. This enabled the mapping of 13 distinct recognition sequences across known RiPP classes. We further validated the ability of AlphaFold to predict precursor peptide interactions with their cognate RRE domains through binding assays to streamline recognition sequence and putative substrate identification. Together, these improvements enhance the accuracy and scope of RRE-Finder, improving access to previously hidden RRE-dependent biosynthetic pathways. IMPORTANCE: Genome mining relies heavily on sequence similarity searches, which severely limit the discovery potential for sequence-divergent proteins. To mitigate this challenge for RRE domain discovery, we employed structure-based alignments to predict sequence-divergent RREs using Foldseek. The newly identified RRE domains were then used to build new HMMs for use by RRE-Finder. This process identified 5,000 previously unidentified but high-confidence RRE domains. Representatives in this sequence-divergent group retain the canonical RRE fold but display new domain fusions, offering additional bioinformatic handles for genome mining. In parallel, AlphaFold 3 modeling of RRE-precursor peptide interactions enabled the identification of 13 distinct recognition sequence motifs, spanning many RiPP biosynthetic pathways. These approaches have significantly expanded the RRE-dependent RiPP biosynthetic landscape.

  PublisherDOI

• Enhancing enzymatic bioconjugation efficiency via installation of a substrate recruitment domain

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-10-27

  preprintOpen access

  Enzyme mediated bioconjugation provides a method for easy and rapid formation of protein-protein and protein-small molecule conjugates under mild conditions. Promiscuous enzymes are of particular interest because they can catalyze conjugation reactions on a broad set of substrates. However, this promiscuity carries the risk of undesirable off-target modifications. To mitigate this effect, we used computational design to install a substrate recruitment domain (SRD) onto the promiscuous enzyme, tyrosinase. The redesigned tyrosinase, called D42, preferentially modifies tyrosine residues within the peptide core (core) linked to a 6-amino acid recognition motif/sequence (RS) specific for the SRD. Incorporation of the recognition sequence along with a neighboring tyrosine in peptides or proteins allows for rapid D42-mediated conversion of the tyrosine to an orthoquinone, which can be selectively modified with a variety of nucleophiles. We demonstrate the utility of our design system by rapidly installing cytotoxic molecules on a monoclonal antibody.

  PublisherOA PDFDOI

• Yerba mate (Ilex paraguariensis) genome provides new insights into convergent evolution of caffeine biosynthesis

  eLife · 2024-12-16 · 6 citations

  articleOpen access

  Yerba mate (YM, Ilex paraguariensis ) is an economically important crop marketed for the elaboration of mate, the third-most widely consumed caffeine-containing infusion worldwide. Here, we report the first genome assembly of this species, which has a total length of 1.06 Gb and contains 53,390 protein-coding genes. Comparative analyses revealed that the large YM genome size is partly due to a whole-genome duplication (Ip-α) during the early evolutionary history of Ilex , in addition to the hexaploidization event (γ) shared by core eudicots. Characterization of the genome allowed us to clone the genes encoding methyltransferase enzymes that catalyse multiple reactions required for caffeine production. To our surprise, this species has converged upon a different biochemical pathway compared to that of coffee and tea. In order to gain insight into the structural basis for the convergent enzyme activities, we obtained a crystal structure for the terminal enzyme in the pathway that forms caffeine. The structure reveals that convergent solutions have evolved for substrate positioning because different amino acid residues facilitate a different substrate orientation such that efficient methylation occurs in the independently evolved enzymes in YM and coffee. While our results show phylogenomic constraint limits the genes coopted for convergence of caffeine biosynthesis, the X-ray diffraction data suggest structural constraints are minimal for the convergent evolution of individual reactions.

  PublisherDOI

Recent grants

• Structural Biological Studies of Thipeptide Biosynthesis and Engineering

  NIH · $1.2M · 2019–2024

• Exploring Peptide Conjugates as Trojan Horse Systems for Drug Design and Discovery

  NIH · $2.2M · 2015–2020

• NIH Grant R56AI117210

  NIH · $467k · 2015

• Mechanistic Studies of Lantibiotic Biosynthetic and Tailoring Enzymes

  NIH · $3.7M · 2006–2024

• NIH Grant P01GM077596

  NIH · $31.1M · 2018

Frequent coauthors

• Wilfred A. van der Donk

  Howard Hughes Medical Institute

  89 shared

• Vinayak Agarwal

  IIT@MIT

  48 shared

• Konstantin Severinov

  Rutgers, The State University of New Jersey

  46 shared

• Isaac Cann

  University of Illinois Urbana-Champaign

  30 shared

• Jonathan R. Chekan

  University of North Carolina at Greensboro

  28 shared

• Douglas A. Mitchell

  Vanderbilt University

  28 shared

• Roderick I. Mackie

  University of Illinois Urbana-Champaign

  25 shared

• D.W. Christianson

  California University of Pennsylvania

  25 shared

Labs

• Center for Biophysics and Quantitative BiologyPI