The crystal structure of Fe₄S₄ quinolinate synthase unravels an enzymatic dehydration mechanism that uses tyrosine and a hydrolase-type triad.

International audienceQuinolinate synthase (NadA) is a Fe4S4 cluster-containing dehydrating enzyme involved in the synthesis of quinolinic acid (QA), the universal precursor of the essential nicotinamide adenine dinucleotide (NAD) coenzyme. A previously determined apo NadA crystal structure revealed the binding of one substrate analog, providing partial mechanistic information. Here, we report on the holo X-ray structure of NadA. The presence of the Fe4S4 cluster generates an internal tunnel and a cavity in which we have docked the last precursor to be dehydrated to form QA. We find that the only suitably placed residue to initiate this process is the conserved Tyr21. Furthermore, Tyr21 is close to a conserved Thr-His-Glu triad reminiscent of those found in proteases and other hydrolases. Our mutagenesis data show that all of these residues are essential for activity and strongly suggest that Tyr21 deprotonation, to form the reactive nucleophilic phenoxide anion, is mediated by the triad. NadA displays a dehydration mechanism significantly different from the one found in archetypical dehydratases such as aconitase, which use a serine residue deprotonated by an oxyanion hole. The X-ray structure of NadA will help us unveil its catalytic mechanism, the last step in the understanding of NAD biosynthesis

Reflections on the Origin and Early Evolution of the Genetic Code

International audienceExamination of the genetic code (GeCo) reveals that amino acids coded by (A/U) codons display a large functional spectrum and bind RNA whereas, except for Arg, those coded by (G/C) codons do not. From a stereochemical viewpoint, the clear preference for (A/U)-rich codons to be located at the GeCo half blocks suggests they were specifically determined. Conversely, the overall lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that i) initially the code was composed of the eight (A/U) codons; ii) these codons were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated; and iii) a combination of A/U and G/C nucleotides progressively generated the remaining codons

The complex roles of adenosine triphosphate in bioenergetics

International audienceATP is generally defined as the "energy currency" of the cell. Its phosphoanhydride P-O bonds are often considered to be "high energy" linkages that release free energy when broken, and its hydrolysis is described as "strongly exergonic". However, breaking bonds cannot release energy and ATP hydrolysis in motor and active transport proteins is not "strongly exergonic". So, the relevance of ATP resides elsewhere. As important as the nucleotide are the proteins that undergo functionally relevant conformational changes upon both ATP binding and release of ADP and inorganic phosphate. ATP phosphorylates proteins for signaling, active transport, and substrates in condensation reactions. The ensuing dephosphorylation has different consequences in each case. In signaling and active transport the phosphate group is hydrolyzed whereas in condensation reactions the phosphoryl fragment acts as a dehydrating agent. As it will be discussed in this article, ATP does much more than simply contribute free energy to biological processes

Reflections on the Origin of Coded Protein Biosynthesis

International audiencefirst_pagesettingsOrder Article ReprintsOpen AccessFeature PaperReviewReflections on the Origin of Coded Protein Biosynthesisby Juan Carlos Fontecilla-CampsUniv. Grenoble Alpes, CEA, CNRS, IBS Metalloproteins Unit, F-38000 Grenoble, FranceBiomolecules 2024, 14(5), 518; https://doi.org/10.3390/biom14050518Submission received: 9 April 2024 / Revised: 23 April 2024 / Accepted: 24 April 2024 / Published: 25 April 2024(This article belongs to the Section Enzymology)Downloadkeyboard_arrow_downBrowse FiguresReview Reports Versions NotesAbstractThe principle of continuity posits that some central features of primordial biocatalytic mechanisms should still be present in the genetically dependent pathway of protein synthesis, a crucial step in the emergence of life. Key bimolecular reactions of this process are catalyzed by DNA-dependent RNA polymerases, aminoacyl-tRNA synthetases, and ribosomes. Remarkably, none of these biocatalysts contribute chemically active groups to their respective reactions. Instead, structural and functional studies have demonstrated that nucleotidic α-phosphate and β-d-ribosyl 2′ OH and 3′ OH groups can help their own catalysis, a process which, consequently, has been called “substrate-assisted”. Furthermore, upon binding, the substrates significantly lower the entropy of activation, exclude water from these catalysts’ active sites, and are readily positioned for a reaction. This binding mode has been described as an “entropy trap”. The combination of this effect with substrate-assisted catalysis results in reactions that are stereochemically and mechanistically simpler than the ones found in most modern enzymes. This observation is consistent with the way in which primordial catalysts could have operated; it may also explain why, thanks to their complementary reactivities, β-d-ribose and phosphate were naturally selected to be the central components of early coding polymers

Nickel and the origin and early evolution of life

International audienceAlthough nickel (Ni) is a minor element of the Earth's crust, it has played a major role in the evolution of life. This metal is a component of the active sites of several archaeal and bacterial anaerobic enzymes essential for bioenergy processes such as H2 and CO oxidation and CO2 fixation. Furthermore, Ni of meteoritic origin was probably involved in primordial organic phosphorylations. However, depending on its concentration, Ni can also be extremely toxic to most species. Through Earth's history this paradoxical situation has provoked complex interactions between microorganisms, such as sulfate-reducing bacteria and the highly Ni-dependent methanogens. Ni-rich volcanic emissions have resulted in alterations of the biological carbon cycle caused by high archaeal production of greenhouse CH4 gas and the ensuing global temperature elevation. These emissions are also thought to have directly helped producing the most serious of the five major extinctions at the end of the Permian period

The stereochemical basis of the genetic code and the (mostly) autotrophic origin of life.

International audienceSpark-tube experiments and analysis of meteorite contents have led to the widespread notion that abiotic organic molecules were the first life components. However, there is a contradiction between the abundance of simple molecules, such as the amino acids glycine and alanine, observed in these studies, and the minimal functional complexity that even the least sophisticated living system should require. I will argue that although simple abiotic molecules must have primed proto-metabolic pathways, only Darwinian evolving systems could have generated life. This condition may have been initially fulfilled by both replicating RNAs and autocatalytic reaction chains, such as the reductive citric acid cycle. The interactions between nucleotides and biotic amino acids, which conferred new functionalities to the former, also resulted in the progressive stereochemical recognition of the latter by cognate anticodons. At this point only large enough amino acids would be recognized by the primordial RNA adaptors and could polymerize forming the first peptides. The gene duplication of RNA adaptors was a crucial event. By removing one of the anticodons from the acceptor stem the new RNA adaptor liberated itself from the stereochemical constraint and could be acylated by smaller amino acids. The emergence of messenger RNA and codon capture followed

Geochemical Continuity and Catalyst/Cofactor Replacement in the Emergence and Evolution of Life

International audienceThe origin of life is mostly divided into "genetics first" and "metabolism first" hypotheses. The former is based on spark-tube tests and organics from meteorites and comets and proposes a heterotrophic origin of life also consistent with the "RNA World" concept. The "metabolism first" hypothesis posits that life began autotrophically on minerals and/or hydrothermal vents. Due to the lack of direct evidence it is not possible to lend solid support to either hypothesis but the "metabolism first" option can be explored if a continuous geochemical, catalytically dynamic process is assumed. Using this approach, I speculate that purine and pyrimidine synthesis originated on a mineral surface, which was later replaced by ATP. The same applies to redox processes where metal bound hydrides could have been replaced by NAD

Primordial bioenergy sources: The two facets of adenosine triphosphate

International audienceLife requires energy to exist, to reproduce and to survive. Two major hypotheses have been put forward concerning the source of this energy at the very early stages of life evolution: (i) abiotic organics either brought to Earth by comets and/or meteorites, or produced at its atmosphere, and (ii) mineral surface-dependent bioinorganic catalytic reactions. Considering the latter possibility, I propose that, besides being a precursor of nucleic acids, adenosine triphosphate (ATP), which probably was used very early to improve the fidelity of nucleic acid polymerization, played an essential role in the transition between mineral-bound protocells and their free counterparts. Indeed, phosphorylation by ATP renders carboxylate groups electrophilic enough to react with nucleophiles such as amines, an effect that, thanks to their Lewis acid character, also have dehydrated metal ions on mineral surfaces. Early ATP synthesis for metabolic processes most likely depended on substrate level phosphorylation. However, the exaptation of a hexameric helicase-like ATPase and a transmembrane H+ pump (which evolved to counteract the acidity caused by fermentation reactions within the protocell) generated a much more efficient membrane-bound ATP synthase that uses chemiosmosis to make ATP

L’univers, les métaux, la vie

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