bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.64898/2026.11.04.763790

The structures of two intermediates en route to DNA repair within a (6-4) photolyase

Yang, C.·Yu, Q.·Cao, X.·Falke, S.·Nan, J.·Beale, E. V.·Chapman, H. N.·Zhong, D.·Lane, T. J.
View original source ↗Export metadata ↓

Abstract

Pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) are mutagenic DNA lesions produced when UV light crosslinks two adjacent pyrimidine bases. These lesions must be repaired to maintain genome integrity, a function executed by the (6-4) photolyase enzymes. This repair chemistry is complex, involving the transfer of a hydroxyl group from one base to another, accompanied or followed by cleavage of an interbase bond. It remains unclear how the enzyme orchestrates this reaction. Typically, models invoke a stepwise process in which an oxetane intermediate is transiently populated, but despite over thirty years of investigation, such an intermediate has never been definitively observed. Conducting dose-controlled X-ray crystallography on the (6-4) photolyase from Vibrio cholerae, we observed the transformation of 6-4PP into an oxetane species. Furthermore, we identified a previously unanticipated hemi-cleaved intermediate. The progressive transformation of 6-4PP into oxetane, hemi-cleaved, and fully repaired species requires a reexamination of the existing models of DNA repair by (6-4) photolyases.

Explore related subjects

biochemistryPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Yang, C., Yu, Q., Cao, X., Falke, S., Nan, J., Beale, E. V., Chapman, H. N., Zhong, D., Lane, T. J.. 2026-11-06. The structures of two intermediates en route to DNA repair within a (6-4) photolyase. https://doi.org/10.64898/2026.11.04.763790

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Endothelial protein C receptor is an entry receptor for Langya virus

Langya virus (LayV) was recently discovered in infected individuals with febrile illness and classified as a Parahenipavirus, a group of poorly understood pathogens. LayV is distantly related to Nipah henipavirus which causes recurring outbreaks with case fatality rates reaching up to 90%. No vaccines or therapeutics are approved for use in humans for any parahenipavirus or henipavirus despite their broad geographic distribution and pandemic potential. Here, we discovered that human endothelial protein C receptor (EPCR) is an entry receptor for LayV and that the tetrameric LayV attachment glycoprotein (G) binds EPCR avidly. We reveal the molecular basis of LayV G recognition of the EPCR receptor and provide a blueprint of the determinants of receptor ortholog usage. We found that human and shrew EPCR orthologs promote cell entry of LayV and of the closely related Mojiang pseudoviruses. These results along with the detection of several Parahenipaviruses in shrews set these pathogens apart from Henipaviruses, which use Pteropid fruit bats as reservoir hosts. Our data support future surveillance efforts, by enabling prediction of EPCR utilization among newly discovered Parahenipaviruses, and the development and evaluation of countermeasures targeting this emerging group of human pathogens.

biochemistry↗
bioRxiv2026

RNA-targeted aminopyridine compounds provide a new antifungal strategy

While RNA is an emerging therapeutic target class, progress is limited by a shortage of well-defined targets in which ligand binding is coupled to measurable function. The group I intron, a self-splicing ribozyme essential in fungal mitochondria but absent from humans, offers both a tractable platform for exploring first principles of small molecule-RNA targeting and a selective antifungal target. We recalibrated an intron-splicing assay to approximate cellular conditions and performed an extensive, cryo-EM-guided structure-activity relationship campaign against the Candida albicans mtLSU intron. Ligands containing a flexible diamine outperformed conformationally constrained analogues, suggesting a general principle for engaging dynamic RNA surfaces and yielding lead aminopyridine 56 (IC 21.6 nM). Compound 56 synergizes with amphotericin B against C. albicans, suggesting a path for combination therapies. RT-qPCR confirmed direct target engagement in cells. This work establishes the fungal group I intron as a viable, mechanistically distinct antifungal target and a model platform for RNA-targeted discovery.

biochemistry↗
bioRxiv2026

Active site electrostatic effects modulate DBO inhibitor potency against OXA-48 variants

The OXA-48 class D {beta}-lactamase and its variants are clinically concerning through their carbapenemase and cephalosporinase activity. Effective inhibitors are therefore urgently needed. Diazabicyclooctanes (DBOs) are newly introduced non {beta}-lactam based inhibitors, but their potency is affected by mutations, with the more recently developed nacubactam consistently less potent than avibactam, the first DBO, towards OXA-48 variants. This difference is most pronounced for OXA-48 compared to its variants OXA-163 and -405, which contain mutations in the {beta}5-{beta}6 loop and preferentially hydrolyse cephalosporins over carbapenems. Here we use multiscale simulations to uncover the origin of these differences after determining that the second step of DBO acylation is rate-limiting. Using QM/MM MD simulations we show that nacubactam exhibits a consistently higher energy barrier than avibactam for covalent inhibition of OXA-48-like enzymes, a difference attributable to DBO-specific changes in the active site electric field. Simulations of non-covalent complexes further indicate that weaker binding, due to electrostatic repulsion between the positively charged nacubactam tail and Arg214 in the {beta}5-{beta}6 loop, partially explains the lower potency of nacubactam towards OXA-48, compared to OXA-163 and -405. Combining computational predictions of covalent reaction rates and non-covalent binding affinities accurately reproduces the relative order of experimental IC50 values, and predicts potency towards OXA-517, a recently discovered OXA-48 variant capable of hydrolysing many antibiotics. This work provides mechanistic insight into the inhibition of class D {beta}-lactamases and reveals the origins of differential DBO potency towards OXA-48 variants, highlighting how subtle differences between enzymes modulate inhibitory effects.

biochemistry↗