Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme

Li, Qiang; Zallot, Rémi; MacTavish, Brian S.; Montoya, Alvaro; Payan, Daniel J.; Hu, Yukun; Gerlt, J.A.; Angerhofer, Alexander; Crécy‐Lagard, Valérie de; Bruner, Steven D.

doi:10.1021/acs.biochem.1c00164

Cited by 7 publications

(6 citation statements)

References 67 publications

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“…Via a series of five enzyme-catalyzed reactions, it starts outside the tRNA with GTP being converted to 7-(aminomethyl)-7-deazaguanine, also referred to as preQ 1 base. − In the next step, the enzyme tRNA-guanine transglycosylase (TGT; EC 2.4.2.29) catalyzes the insertion of this intermediate into tRNA, which occurs in exchange for the genetically encoded guanine . Thereupon, at the tRNA level and mediated by the enzyme tRNA preQ 1 -34 S -adenosylmethionine ribosyltransferase-isomerase (QueA), the exocyclic aminomethyl group of preQ 1 is endowed with an epoxy-dihydroxy-cyclopentyl moiety originating from the ribose of S -adenosyl- l -methionine. , Eventually, the epoxide within the attached five-membered ring is reduced to a double bond by the enzyme epoxyqueuosine reductase. , …”

Section: Introductionsupporting

confidence: 88%

“…10,11 Eventually, the epoxide within the attached five-membered ring is reduced to a double bond by the enzyme epoxyqueuosine reductase. 12,13 Facilitated by the high-resolution crystal structure of the TGT from Zymomonas mobilis, 14 the bacterial TGT has been well investigated. It constitutes a homodimer with each subunit featuring a (βα) 8 barrel fold extended by a three-stranded antiparallel β sheet at its N-terminus and by an extra α helix at its C-terminus.…”

Section: ■ Introductionmentioning

confidence: 99%

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Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase

et al. 2022

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In tRNAAsp, tRNAAsn, tRNATyr, and tRNAHis of most bacteria and eukaryotes, the anticodon wobble position may be occupied by the modified nucleoside queuosine, which affects the speed and the accuracy of translation. Since eukaryotes are not able to synthesize queuosine de novo, they have to salvage queuine (the queuosine base) as a micronutrient from food and/or the gut microbiome. The heterodimeric Zn2+ containing enzyme tRNA-guanine transglycosylase (TGT) catalyzes the insertion of queuine into the above-named tRNAs in exchange for the genetically encoded guanine. This enzyme has attracted medical interest since it was shown to be potentially useful for the treatment of multiple sclerosis. In addition, TGT inactivation via gene knockout leads to the suppressed cell proliferation and migration of certain breast cancer cells, which may render this enzyme a potential target for the design of compounds supporting breast cancer therapy. As a prerequisite to fully exploit the medical potential of eukaryotic TGT, we have determined and analyzed a number of crystal structures of the functional murine TGT with and without bound queuine. In addition, we have investigated the importance of two residues of its non-catalytic subunit on dimer stability and determined the Michaelis–Menten parameters of murine TGT with respect to tRNA and several natural and artificial nucleobase substrates. Ultimately, on the basis of available TGT crystal structures, we provide an entirely conclusive reaction mechanism for this enzyme, which in detail explains why the TGT-catalyzed insertion of some nucleobases into tRNA occurs reversibly while that of others is irreversible.

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Section: Introductionsupporting

confidence: 88%

Section: ■ Introductionmentioning

confidence: 99%

Structural and Biochemical Investigation of the Heterodimeric Murine tRNA-Guanine Transglycosylase

et al. 2022

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“…In bacteria, genes for enzymes involved in successive biosynthetic routes are often physically clustered, and it was this assumption that was tested to search for genes near tgt and queA in organisms that did not possess q ueG . This approach successfully identified a new class of enzyme called QueH that is cobalamin independent and functions with a single 4Fe–4S cluster and an additional undefined metal to catalyze the conversion of oQ 34 to Q 34 . In the case of QueH, the postulated mechanism differs from that of QueG and involves a novel protonation-assisted radical mechanism with the intervention of a transient carbanion (Figure ), a challenging chemistry that requires more extensive experimental validation.…”

Section: Comparative Genomics a Powerful Approach In The Search For A...mentioning

confidence: 99%

Integrative Approach to Probe Alternative Redox Mechanisms in RNA Modifications

Bou-Nader,

Pecqueur,

de Crécy-Lagard

et al. 2023

Acc. Chem. Res.

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Conspectus RNA modifications found in most RNAs, particularly in tRNAs and rRNAs, reveal an abundance of chemical alterations of nucleotides. Over 150 distinct RNA modifications are known, emphasizing a remarkable diversity of chemical moieties in RNA molecules. These modifications play pivotal roles in RNA maturation, structural integrity, and the fidelity and efficiency of translation processes. The catalysts responsible for these modifications are RNA-modifying enzymes that use a striking array of chemistries to directly influence the chemical landscape of RNA. This diversity is further underscored by instances where the same modification is introduced by distinct enzymes that use unique catalytic mechanisms and cofactors across different domains of life. This phenomenon of convergent evolution highlights the biological importance of RNA modification and the vast potential within the chemical repertoire for nucleotide alteration. While shared RNA modifications can hint at conserved enzymatic pathways, a major bottleneck is to identify alternative routes within species that possess a modified RNA but are devoid of known RNA-modifying enzymes. To address this challenge, a combination of bioinformatic and experimental strategies proves invaluable in pinpointing new genes responsible for RNA modifications. This integrative approach not only unveils new chemical insights but also serves as a wellspring of inspiration for biocatalytic applications and drug design. In this Account, we present how comparative genomics and genome mining, combined with biomimetic synthetic chemistry, biochemistry, and anaerobic crystallography, can be judiciously implemented to address unprecedented and alternative chemical mechanisms in the world of RNA modification. We illustrate these integrative methodologies through the study of tRNA and rRNA modifications, dihydrouridine, 5-methyluridine, queuosine, 8-methyladenosine, 5-carboxymethylamino-methyluridine, or 5-taurinomethyluridine, each dependent on a diverse array of redox chemistries, often involving organic compounds, organometallic complexes, and metal coenzymes. We explore how vast genome and tRNA databases empower comparative genomic analyses and enable the identification of novel genes that govern RNA modification. Subsequently, we describe how the isolation of a stable reaction intermediate can guide the synthesis of a biomimetic to unveil new enzymatic pathways. We then discuss the usefulness of a biochemical “shunt” strategy to study catalytic mechanisms and to directly visualize reactive intermediates bound within active sites. While we primarily focus on various RNA-modifying enzymes studied in our laboratory, with a particular emphasis on the discovery of a SAM-independent methylation mechanism, the strategies and rationale presented herein are broadly applicable for the identification of new enzymes and the elucidation of their intricate chemistries. This Account offers a comprehensive glimpse into the evolving landscape of RNA modification research and highlights the ...

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“…The epoxide moiety of epoxyqueuosine is reduced by widely conserved metalloenzyme QueH or cobalamindependent enzyme QueG to give queuosine. 172,173…”

Section: Biosynthesis Of Queuosinementioning

confidence: 99%