Hyunbin Lee

All Publications

• Diverse bacterial pattern recognition receptors sense the conserved phage proteome. bioRxiv : the preprint server for biology Lee, H., Luengo-Woods, S., Zhang, J., Makarova, K. S., Wolf, Y. I., Chiu, C., Evans, S. A., Chen, J., Xiao, H., Feng, L., Koonin, E. V., Gao, A. 2026

  Abstract

  Recognition of foreign molecules inside cells is critical for immunity in all domains of life. Proteins of the STAND NTPase superfamily, including eukaryotic nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs), play a central role in this process. In bacteria and archaea, although several STAND NTPase families have been reported to sense phage proteins, their functional diversity remains largely unexplored. Here, we conducted a systematic phylogenetic analysis of prokaryotic STAND NTPases and identified at least 90 structurally distinct families associated with antiviral defense. We first show that the uncharacterized Avs7 family recognizes the major capsid protein (MCP) of tailed phages. Three cryo-EM structures of Salmonella enterica Avs7 reveal an asymmetric, butterfly-shaped tetramer that assembles stepwise via large, MCP-induced conformational changes, incorporating bacterial translation elongation factor Tu (EF-Tu) as a scaffold that is required for full defense activity. Using highly parallel genetic screens, we further show that 13 additional STAND families sense 12 conserved phage protein folds, encompassing most of the core structural and replicative components of tailed phages. These include two structurally distinct families-Avs8 (PD-λ-4) and Avs10 (Erebus/Hypnos/bNACHT64)-that also recognize MCP, as well as 11 other families (Avs11-21) that recognize the portal, portal adaptor, tail nozzle, head-tail connector, tail terminator, tail tube protein, tail assembly chaperone, tape measure protein, DNA polymerase, helicase/RecA-type ATPase, and single-stranded DNA annealing protein (SSAP), respectively. Together, our findings highlight structure-based pattern recognition and host factor repurposing as fundamental strategies of bacterial immunity.

  View details for DOI 10.64898/2026.01.04.697583

  View details for PubMedID 41542633

  View details for PubMedCentralID PMC12803255

• Unique structural and ligand binding properties of the Staphylococcus aureus serine hydrolase FphE. bioRxiv : the preprint server for biology Jo, J., Upadhyay, T., You, X., Bennett, J. M., Lee, H., Bogyo, M., Fellner, M. 2025

  Abstract

  Staphylococcus aureus is a human pathogen capable of forming biofilms that complicate treatment and facilitate chronic infections. A family of S. aureus serine hydrolases are important regulators of virulence and biofilm formation. Among these, FphE is highly specific to S. aureus and therefor a viable target for both imaging and therapy. Here, we present bioinformatic and structural evidence that FphE may be involved in aromatic compound metabolism. In addition, twelve distinct crystal forms reveal that FphE exists as a highly unusual but stable and flexible, cross-subunit homodimer, unique to the large alpha/beta hydrolase superfamily. Substrate engagement favors retention of the dimeric state, which is a more catalytically active form of the enzyme and small angle X-ray scattering (SAXS) confirms the dimeric architecture occurs in solution. High-resolution co-crystal structures of FphE covalently bound to two chemically distinct ligands reveal different modes of active site engagement, supporting an atypical structural plasticity of the dimer interface. Together, these findings establish FphE as a structurally unique alpha/beta hydrolase and provide a foundation for structure-guided development of S. aureus specific inhibitors and imaging probes.

  View details for DOI 10.1101/2025.10.12.681921

  View details for PubMedID 41280051

  View details for PubMedCentralID PMC12632446

• Discovery of a Two-Step Enzyme Cascade Converting Aspartate to Aminomalonate in Peptide Natural Product Biosynthesis JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Kim, H., Kang, S., Kim, S., Lee, H., Hur, Y., Song, W., Oh, D., Kim, S. 2025

  Abstract

  Aminomalonic acid (Ama) is found in various natural products and protein hydrolysates of multiple organisms, but the understanding of its biosynthetic origin remains largely limited. By exploiting a biosynthetic gene cluster for ribosomally synthesized and post-translationally modified peptides (RiPPs), which are rich sources of new enzyme chemistry, we identified a novel two-enzyme pathway for Ama biosynthesis. This biosynthetic pathway, mediated by an Fe(II)/2-oxoglutarate-dependent oxygenase (Fe(II)/2OG), SmaO, and an atypical Fe(II)-dependent histidine-aspartate (HD) domain enzyme, SmaX, converts aspartate (Asp) to β-hydroxyaspartic acid (Hya) intermediate and ultimately to Ama. These tandem enzymatic reactions─hydroxylation of the carbon next to an acid functional group and subsequent four-electron oxidative bond cleavage in α-hydroxy acid─are similar to those associated with other known HD domain oxygenases, PhnZ and TmpB. However, SmaX also exhibits unique features, such as C-C bond cleavage in α-hydroxycarboxylate using a single Fe cofactor, in contrast to the C-P bond cleavage using a mixed-valent diiron cofactor in PhnZ and TmpB. Bioinformatic analysis reveals that this two-enzyme cascade may be present in various biosynthetic pathways for peptide natural products, including RiPPs and nonribosomal peptides (NRPs). Collectively, our study demonstrates the presence of a novel Ama biosynthetic pathway and suggests its widespread distribution in peptide natural product biosynthesis.

  View details for DOI 10.1021/jacs.5c05071

  View details for Web of Science ID 001503504200001

  View details for PubMedID 40473404

• Naturally ornate RNA-only complexes revealed by cryo-EM. Nature Kretsch, R. C., Wu, Y., Shabalina, S. A., Lee, H., Nye, G., Koonin, E. V., Gao, A., Chiu, W., Das, R. 2025

  Abstract

  Myriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures1-4. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryogenic electron microscopy at resolutions of 2.9-3.1 Å. Without precedent among previously characterized natural RNA molecules, Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD), Rumen-Originating, Ornate, Large (ROOL), and Ornate Large Extremophilic (OLE) RNAs form homo-oligomeric complexes whose stoichiometries are retained at concentrations lower than expected in the cell. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome, empty except for a disordered loop. Extensive intra- and intermolecular A-minor interactions, kissing loops, an unusual A-A helix, and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.

  View details for DOI 10.1038/s41586-025-09073-0

  View details for PubMedID 40328315