Kissman EN, Kipouros I, Slater JW
… +10 more, Stone EA, Yang AY, Braun A, Ensberg AR, Whitten AM, Chatterjee K, Bogacz I, Yano J, Martin Bollinger J, Chang MCY
Nat Chem Biol
· 2026 Mar · PMID 41272319
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The activation of inert C(sp)-H bonds by nonheme Fe enzymes provides a powerful biocatalytic platform for the chemical synthesis of molecules with increased sp complexity. In this context, Fe/α-ketoglutarate-dependent ra...The activation of inert C(sp)-H bonds by nonheme Fe enzymes provides a powerful biocatalytic platform for the chemical synthesis of molecules with increased sp complexity. In this context, Fe/α-ketoglutarate-dependent radical halogenases are uniquely capable of carrying out transfer of a diverse array of bound anions following C-H activation. Here, we provide experimental evidence that bifurcation of radical rebound after H-atom abstraction can be driven both by the ability of a dynamic metal coordination sphere to reorganize and by a second-sphere hydrogen-bonding network where only two residues are sufficient. In addition, we present crystallographic data supporting the existence of an early peroxyhemiketal intermediate in the O activation pathway of Fe/α-ketoglutarate-dependent enzymes. These data provide a paradigm for understanding the evolution of catalytic plasticity in these enzymes and yields insight into the design principles by which to expand their reaction scope.
Upon sensing nonself target RNA, the CorA-associated type III-B CRISPR-Cas system catalyzes S-adenosyl methionine (SAM) and ATP to synthesize SAM-AMP, which activates the effector CorA and triggers immune responses. SAM-...Upon sensing nonself target RNA, the CorA-associated type III-B CRISPR-Cas system catalyzes S-adenosyl methionine (SAM) and ATP to synthesize SAM-AMP, which activates the effector CorA and triggers immune responses. SAM-AMP can be degraded by NrN and SAM lyase, potentially deactivating the system. Here we find that the type III-B effector complex from Bacteroides fragilis uses a specific mechanism to recognize nonself target RNA and synthesize SAM-AMP. The 3' anti-tag of nonself target RNA induces conformational changes in the Cmr2 subunit, triggering SAM-AMP synthesis independently of the stalk loop of Cmr3 subunit. SAM-AMP binding induces NrN to transit from an open to a closed conformation, enabling hydrolysis of the 3'-5' phosphodiester bond. SAM lyase forms a triangular trimer that specifically degrades SAM-AMP into 5'-methylthioadenosine-AMP and homoserine lactone. These findings unveil unique mechanisms for SAM-AMP synthesis and degradation and provide deeper insights into the molecular basis of type III CRISPR-Cas signaling.
Lin Z, Ngo W, Chou YT
… +6 more, Wu H, Susa KJ, Jun YW, Bivona TG, Doudna JA, Wells JA
Nat Chem Biol
· 2026 Feb · PMID 41254216
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Photoproximity labeling proteomics (PLP) methods have recently shown that cell surface receptors can form lateral interactome networks. Here, we present a paired set of PLP workflows that dynamically track neighborhood c...Photoproximity labeling proteomics (PLP) methods have recently shown that cell surface receptors can form lateral interactome networks. Here, we present a paired set of PLP workflows that dynamically track neighborhood changes for oncogenic epidermal growth factor receptor (EGFR) over time, both outside and inside of cells. We achieved this by augmenting the multiscale PLP workflow we call MultiMap, where three photoprobes with different labeling ranges were photoactivated by one photocatalyst, eosin Y, anchored extracellularly and intracellularly on EGFR. We identified hundreds of neighboring proteins that changed within minutes to over 1 h after the addition of EGF. These neighborhoods reveal dynamic interactomes during early, middle and late signaling that drive phosphorylation, internalization, degradation and transcriptional regulation. This rapid 'molecular photographic' labeling approach provides snapshots of signaling neighborhoods, revealing their dynamic nature and potential for drug targeting.
Nitrogenase catalyzes atmospheric nitrogen fixation, a critical biological process that depends on an intricate organometallic cofactor assembled by a dedicated multiprotein system. Here we uncover the structural basis f...Nitrogenase catalyzes atmospheric nitrogen fixation, a critical biological process that depends on an intricate organometallic cofactor assembled by a dedicated multiprotein system. Here we uncover the structural basis for the function of NifEN, the scaffold protein that mediates the final stages of cofactor biosynthesis before its incorporation into nitrogenase. High-resolution structural analyses reveal that the cofactor precursor initially binds at a surface docking site before being transferred into a specialized cavity for further maturation. This process involves dynamic structural rearrangements, including coordinated domain motions and partial unfolding, enabling the scaffold to alternate between open and closed states. Additionally, a rear channel extends to the precursor-binding cavity, likely facilitating the entry of the modifying components molybdenum and homocitrate. These findings illuminate the dynamic mechanisms underlying FeMo-cofactor assembly and underscore the functional divergence between NifEN, the biosynthetic scaffold, and NifDK, the catalytic component of nitrogenase.
Ubiquitin-dependent protein degradation regulates myriad fundamental cellular processes. At its core are degradation signals, or degrons, that initiate substrate engagement and ubiquitination by E3 ubiquitin ligases. Her...Ubiquitin-dependent protein degradation regulates myriad fundamental cellular processes. At its core are degradation signals, or degrons, that initiate substrate engagement and ubiquitination by E3 ubiquitin ligases. Here we highlight how a variety of degradation signals promote substrate-E3 ligase interactions to orchestrate protein turnover with precision. While short linear motifs are frequently identified as degrons, an increasing number of degrons have recently been mapped to high-order protein structures, underscoring the architectural diversity and cryptic nature of degradation signals. Furthermore, nonproteinaceous signals beyond degrons often facilitate the precise control of protein ubiquitination. These additional signals can reside within substrates and E3 ligases or at their interfaces. Finally, we discuss how dysregulation of degrons and degradation signals is linked to human diseases. A deeper mechanistic understanding of degradation signals will guide new therapeutic strategies, whether by restoring defective protein ubiquitination or by harnessing targeted protein degradation.
Dell M, Kogawa M, Streiff AB
… +25 more, Shiraishi T, Lotti A, Meier CM, Schorn MA, Field C, Cahn JKB, Yokoyama H, Yamada Y, Peters E, Egami Y, Nakashima Y, Tan KC, Rückert C, Alanjary M, Kalinowski J, Kuzuyama T, Cardenas P, Pomponi S, Sipkema D, Wright A, Takada K, Abe I, Wakimoto T, Takeyama H, Piel J
Nat Chem Biol
· 2026 Feb · PMID 41233523
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Marine sponges are the source of numerous bioactive natural products that serve as chemical defenses and provide pharmaceutical leads for drug development. For some of the compounds, symbiotic bacteria have been establis...Marine sponges are the source of numerous bioactive natural products that serve as chemical defenses and provide pharmaceutical leads for drug development. For some of the compounds, symbiotic bacteria have been established as the actual producers. Among the known sponge symbionts, 'Candidatus Entotheonella' members stand out because of their abundant and variable biosynthetic gene clusters (BGCs). Here, to obtain broader insights into this producer taxon, we conduct a comparative analysis on eight sponges through metagenomic and single-bacterial sequencing and biochemical studies. The data suggest sets of biosynthetic genes that are largely unique in 14 'Entotheonella' candidate species and a member of a sister lineage named 'Candidatus Proxinella'. Four biosynthetic loci were linked in silico or experimentally to cytotoxins, antibiotics and the terpene cembrene A from corals. The results support widespread and diverse bacterial roles in the chemistry of sponges and aid the development of sustainable production methods for sponge-derived therapeutics.
Nat Chem Biol
· 2026 Feb · PMID 41193830
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Structure-based drug discovery relies on three-dimensional protein structures to provide the atomic blueprints for small-molecule design, indicating where to place each atom to maximize favorable interactions. The advent...Structure-based drug discovery relies on three-dimensional protein structures to provide the atomic blueprints for small-molecule design, indicating where to place each atom to maximize favorable interactions. The advent of cryo-cooling crystals in crystallography greatly accelerated the ease and accessibility of structural data, making it a mainstay of most drug discovery efforts. However, despite its successes, including producing numerous clinically successful molecules, cryo-cooled samples only tell part of the structural story: they may leave out dynamic details or introduce artifacts that may lead drug discovery campaigns astray. In this Perspective, we highlight recent studies characterizing temperature-sensitive structural phenomena observed by crystallography. We showcase how leveraging information on rare, hidden conformational states informs ligand discovery via molecular docking. This demonstrates the value of performing structural studies at elevated temperatures, closer to where biology occurs, to 'unfreeze' structural ensembles for drug discovery and design.