Search bioRxiv⌕ Search

bioRxiv · 10.1101/2024.05.04.592530

Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction

Abstract

In a continuing effort to understand reaction mechanisms of terpene synthases catalyzing initial anti-Markovnikov cyclization reactions, we solved the X-ray crystal structure of (+)-caryolan-1-ol synthase (CS) from Streptomyces griseus, with and without an inactive analog of the FPP substrate, 2-fluorofarnesyl diphosphate (2FFPP), bound in the active site of the enzyme. The CS-2FFPP complex was solved to 2.65 [A] resolution and showed the ligand in a linear, elongated orientation, incapable of undergoing the initial cyclization event to form a bond between carbons C1 and C11. Intriguingly, the apo CS structure (2.2 [A]) also had electron density in the active site, in this case density that was well fit with a curled-up tetraethylene glycol molecule presumably recruited from the crystallization medium. The density was also well fit by a molecule of farnesene suggesting that the structure may mimic an intermediate along the reaction coordinate. The curled-up conformation of tetraethylene glycol was accompanied by dramatic rotamer shifts among active-site residues. Most notably, W56 was observed to undergo a 90{degrees} rotation between the 2FFPP complex and apo-enzyme structures, suggesting that it contributes to steric interactions that help curl the tetraethylene glycol molecule in the active site, and by extension perhaps also a derivative of the FPP substrate in the normal course of the cyclization reaction. In support of this proposal, the CS W56L variant lost the ability to cyclize the FPP substrate and produced only the linear terpene products farnesol and - and {beta}-farnesene.

Source connections

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Ramasamy, P. K., Matos, J. O., Black, B. Y., Ellenburg, W. H., Chen, J., Patterson, M., Gehtman, J. A., Theobald, D., Krauss, I. J., Oprian, D. D.. 2024-05-05. Crystal Structure of Caryolan-1-ol Synthase, a Sesquiterpene Synthase Catalyzing an Initial Anti-Markovnikov Cyclization Reaction. https://doi.org/10.1101/2024.05.04.592530

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

KEEP EXPLORING

Related preprints

Impacts of Environmental Nickel and Chromium Exposure on the Blood Proteome of House Sparrows (Passer domesticus) in New Caledonia

New Caledonia holds some of the world's largest ultramafic mineral deposits, and nickel (Ni) smelting operations have created a gradient of Ni and chromium (Cr) contamination across the archipelago. Molecular impacts of Ni and Cr toxicity on wildlife remain largely unexplored. Here, we used the house sparrow (Passer domesticus) as a sentinel species to characterise the blood proteomic response to Ni and Cr exposure near the Doniambo smelter in Noumea. Blood was collected from 52 free-living sparrows across 18 sites classified by soil metal concentration. Plasma and blood cell pellet fractions were analysed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Plasma proteomics identified histidine-rich glycoprotein (HRG) as the most prominent responder, with approximately 2.1-fold elevation in exposed relative to low-exposure birds. HRG contains a conserved histidine-rich region that binds cations including divalent nickel, and paired plasma-liver analysis confirmed hepatic-driven synthesis. Blood cell pellet proteomics revealed that Ni-Cr co-exposure predominantly disrupts the nuclear compartment: histone depletion indicated chromatin collapse, NUP153 dysregulation impaired nuclear pore function, and VRK1/TRIP13 upregulation suggested DNA damage response activation coupled with mitotic checkpoint override. Concurrent RNA processing collapse (DDX17, DHX15, RBMX, ALYREF) and changes in telomere-associated proteins (TERF2IP, hnRNPA1 and VRK1) implicated disrupted genome maintenance. These findings identify HRG as a candidate plasma biomarker of Ni-Cr exposure and reveal a coordinated nuclear toxicity signature linking heavy metal contamination to DNA damage and epigenetic disruption in a free-living vertebrate.

biochemistry↗

Programmable amide bond formation using de novo ligases

Amide bond formation is of central importance in the chemical industry, underpinning the synthesis of small bioactive molecules, macrocycles, peptides and their conjugates. Conventional methods of amide synthesis rely on stoichiometric coupling agents and costly protecting group manipulations. While biocatalysis can alleviate some of these challenges, enzymes typically operate across a narrow range of substrates and their adaptation to new coupling partners requires extensive engineering. Here we show that de novo amide ligases featuring a cysteine catalytic triad can be programmed computationally to operate across diverse substrate classes with high selectivity. We first designed complementary peptide ligases to selectively functionalise either the N-terminus or a single lysine residue of a polypeptide sequence containing 36 competing lysines. Crystal structures of both ligases show excellent agreement with the designs, with structural modelling suggesting that amidation outcompetes hydrolysis because the catalytically competent geometry forms only upon acceptor binding. We then extended our approach to the synthesis of small bioactive molecules by designing stereoselective ligases that mediate a key amide bonding forming step in the synthesis of the preventative HIV therapeutic lenacapavir. These results establish de novo enzyme design as a programmable platform for achieving selective amide bond formations across a wide range of molecular targets.

biochemistry↗

De novo design of ligases for programmable site-specific protein ubiquitylation

Protein ubiquitylation regulates numerous cellular processes, but difficulties in generating site-specifically ubiquitylated proteins limit our understanding of individual modification events. In cells, ubiquitylation is mediated by an E1-E2-E3 enzyme cascade, with substrate recognition largely determined by more than 600 human E3 ligases, making it challenging to redirect ubiquitin transfer to a chosen lysine. Here we use RFdiffusion3 to design ubiquitin ligases from scratch that use a cysteine-based catalytic triad to conjugate an activated ubiquitin donor to a selected lysine in a chosen target substrate. Of 48 tested designs, 35 ubiquitylated a model peptide, with the most active ligases achieving near-quantitative ubiquitin transfer. We next challenged the approach with the homotrimeric sliding clamp proliferating cell nuclear antigen (PCNA), whose ubiquitylation at lysine (K) 164 governs DNA damage tolerance while displaying 45 off-target lysines for ubiquitination. Screening of 48 designs delivered a site-selective ligase. Incorporation of a single activity-increasing substitution and coupling to E1-dependent donor activation resulted in 90% conversion from unactivated ubiquitin, delivering higher rates and superior selectivity compared to a natural promiscuous E2. Using this cascade, we transferred di-, tri- and tetraubiquitin chains of defined length to PCNA K164 through a native isopeptide bond. These results establish de novo enzyme design as a route towards programmable, site-specific protein ubiquitylation. That a single de novo designed protein can bind both an activated ubiquitin donor and a globular target, and use a proficient catalytic machinery to selectively transfer ubiquitin to one lysine among 45, illustrates the level of functional complexity now within reach of de novo enzyme design.

biochemistry↗