9DCO

Crystal structure of epoxyqueuosine reductase QueH D13N mutant from Thermotoga maritima

Summary for 9DCO

• Entry DOI: 10.2210/pdb9dco/pdb
• Descriptor: Epoxyqueuosine reductase QueH, IRON/SULFUR CLUSTER, ZINC ION, ... (5 entities in total)
• Functional Keywords: queuosine biosynthesis, epoxyqueuosine reductase, metal binding protein
• Biological source: Thermotoga maritima MSB8
• Total number of polymer chains: 1
• Total formula weight: 23000.39

Authors

Hu, Y.,Bruner, S.D. (deposition date: 2024-08-27, release date: 2024-12-18, Last modification date: 2025-02-05)

Primary citation

Hu, Y.,Jaroch, M.,Sun, G.,Dedon, P.C.,de Crecy-Lagard, V.,Bruner, S.D.
Mechanism of Catalysis and Substrate Binding of Epoxyqueuosine Reductase in the Biosynthetic Pathway to Queuosine-Modified tRNA.
Biochemistry, 64:458-467, 2025

PubMed Abstract: Post-transcriptional modifications at the anticodon stem-loop of tRNAs are key to the translation function. Metabolic pathways to these modifications often incorporate complex enzymology. A notable example is the hypermodified nucleoside, queuosine, found at the wobble position of Asn, Asp, His, and Tyr encoding tRNAs. The epoxyqueuosine reductase, QueH, catalyzes the final step in the biosynthetic pathway to queuosine. The metalloenzyme catalyzes a two-electron reduction of epoxyqueuosine to provide the modified tRNA. The structure of QueH from has previously been determined and unexpectedly contains two metal binding motifs in the active site. This includes a predicted 4Fe-4S cluster, along with a single-metal binding site coordinated by two cysteines along an aspartate carboxylate. In this report, we describe the structural and biochemical analysis of the QueH metal binding sites along with the chemistry of epoxide deoxygenation. To probe the active-site architecture, enzyme mutants of metal binding residues were structurally and biochemically characterized. In addition, structural and binding experiments were used to probe interactions of QueH with tRNA and the in vivo role of QueH and variants in Q-tRNA synthesis was evaluated. Overall, this work provides insight into the chemical mechanism of the final step of the queuosine biosynthetic pathway.

PubMed: 39644232
DOI: 10.1021/acs.biochem.4c00524

Experimental method

X-RAY DIFFRACTION (2.11 Å)