A Single Adenosine with a Neutral p
            <i>K</i>
            <sub>a</sub>
            in the Ribosomal Peptidyl Transferase Center

Muth, Gregory W.; Ortoleva-Donnelly, Lori; Strobel, Scott A.

doi:10.1126/science.289.5481.947

Cited by 246 publications

(181 citation statements)

References 30 publications

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“…The proximity of the N3 of A2486 (2451 in Escherichia coli) to the attacking ␣ amino group and the analogue of the tetrahedral intermediate led to the suggestion that A2486 (2451) may function as a general acid͞base during peptide bond formation. This hypothesis appeared to be supported by data on the pH dependence of its chemical reactivity and the finding that mutations of A2486 are dominant lethal in vivo (12). Further, the interaction between the N3 of A2486 (2451) and the phosphate oxygen of the reaction intermediate observed in the structure implied an altered pKa (8).…”

supporting

confidence: 60%

Structural insights into peptide bond formation

Tm²,

Pb³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

269

232

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The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl-and peptidyl-RNA fragments of tRNA. We have refined at 3-Å resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The ␣-NH2 group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2 OH of the A-76 ribose in the P site or with the 2 OH of A2486 (2451). These interactions position the ␣ amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.

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supporting

confidence: 60%

Structural insights into peptide bond formation

Tm²,

Pb³

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

269

232

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“…We found that twister does not have a HB donor with good geometry and a chemical group with a reasonable pK A to act as a general acid. The only HB donor with reasonable geometry is the N3 of A10, but this nitrogen has a very low pK A of about -4.2 to 1.0 (22,23). Although this would be a great chemical group to interact with the 5′-OH leaving group, it would require a highly perturbed pK A to act as a general acid.…”

Section: Discussionmentioning

confidence: 99%

Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme

Eiler¹,

Wang²,

Steitz

2014

Proc. Natl. Acad. Sci. U.S.A.

142

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Twister is a recently discovered RNA motif that is estimated to have one of the fastest known catalytic rates of any naturally occurring small self-cleaving ribozyme. We determined the 4.1-Å resolution crystal structure of a twister sequence from an organism that has not been cultured in isolation, and it shows an ordered scissile phosphate and nucleotide 5′ to the cleavage site. A second crystal structure of twister from Orzyza sativa determined at 3.1-Å resolution exhibits a disordered scissile phosphate and nucleotide 5′ to the cleavage site. The core of twister is stabilized by base pairing, a large network of stacking interactions, and two pseudoknots. We observe three nucleotides that appear to mediate catalysis: a guanosine that we propose deprotonates the 2′-hydroxyl of the nucleotide 5′ to the cleavage site and a conserved adenosine. We suggest the adenosine neutralizes the negative charge on a nonbridging phosphate oxygen atom at the cleavage site. The active site also positions the labile linkage for in-line nucleophilic attack, and thus twister appears to simultaneously use three strategies proposed for small self-cleaving ribozymes. The twister crystal structures (i) show its global structure, (ii) demonstrate the significance of the double pseudoknot fold, (iii) provide a possible hypothesis for enhanced catalysis, and (iv) illuminate the roles of all 10 highly conserved nucleotides of twister that participate in the formation of its small and stable catalytic pocket.X-ray crystallography | RNA structure | weak derivative phasing | samarium derivatives | cesium derivatives T he twister RNA motif was identified by bioinformatic searches and then validated biochemically to be a small self-cleaving ribozyme (1). This recently discovered class of ribozymes is called twister because its conserved secondary structure resembles the ancient Egyptian hieroglyph "twisted flax." Representatives of the twister ribozyme class are found in all domains of life, but its biological role has yet to be determined. In addition to twister, the small self-cleaving ribozyme family includes the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), and glmS ribozymes (the glmS ribozyme is upsteam of the the glmS gene that codes for the enzyme that catalyzes glucosamine-6-phosphate production) (1-6).The small self-cleaving ribozyme family can be split into two groups based on whether their active site is formed by an irregular helix (hammerhead, hairpin, and VS) or a double pseudoknot (PK) structure (HDV and glmS) (7). The structures of HDV and glmS are known, whereas twister was predicted from representative sequences to use two PKs to form its active site. It was expected that twister would be smaller in size than either HDV or glmS and more comparable in size and complexity to hammerhead (1).The self-cleavage rate constant of twister is estimated to be as rapid as or slightly more rapid than the hammerhead ribozyme. The estimated rate constants (k obs ) for twister is 1,000 per minute, and the experime...

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“…Among the myriad of molecules that existed in the RNA-world, a population of them was involved in the origin of translation, whereby it has been sensibly suggested that the original function of the ribosome was RNA replication via triplets, not translation . We can take it as a given that at some point a precursor of the peptidyl transferase reaction (Muth et al 2000) of an RNA molecule did evolve, and the chance stereochemistry of that molecule would determine the decision of whether it could catalyse the polymerization of d-or lamino acids into peptides. That filter would be sufficient to tip the holochirality scale, because despite the presence of a racemate, only amino acids of the same a-carbon configuration would preferentially end up in peptides, yielding a population of distinctly handed peptides, some of which would eventually need to feed back in a hypercycle-like manner (Eigen & Schuster 1978) into favoured synthesis of their stereochemically correct polymerizing template.…”

Section: Holochiralitymentioning

confidence: 99%

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

Martin

Russell

2003

Phil. Trans. R. Soc. Lond. B

731

621

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All life is organized as cells. Physical compartmentation from the environment and self-organization of self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life's most likely forebear. We propose that life evolved in structured iron monosulphide precipitates in a seepage site hydrothermal mound at a redox, pH and temperature gradient between sulphide-rich hydrothermal fluid and iron(II)-containing waters of the Hadean ocean floor. The naturally arising, three-dimensional compartmentation observed within fossilized seepage-site metal sulphide precipitates indicates that these inorganic compartments were the precursors of cell walls and membranes found in free-living prokaryotes. The known capability of FeS and NiS to catalyse the synthesis of the acetyl-methylsulphide from carbon monoxide and methylsulphide, constituents of hydrothermal fluid, indicates that pre-biotic syntheses occurred at the inner surfaces of these metal-sulphide-walled compartments, which furthermore restrained reacted products from diffusion into the ocean, providing sufficient concentrations of reactants to forge the transition from geochemistry to biochemistry. The chemistry of what is known as the RNA-world could have taken place within these naturally forming, catalyticwalled compartments to give rise to replicating systems. Sufficient concentrations of precursors to support replication would have been synthesized in situ geochemically and biogeochemically, with FeS (and NiS) centres playing the central catalytic role. The universal ancestor we infer was not a free-living cell, but rather was confined to the naturally chemiosmotic, FeS compartments within which the synthesis of its constituents occurred. The first free-living cells are suggested to have been eubacterial and archaebacterial chemoautotrophs that emerged more than 3.8 Gyr ago from their inorganic confines. We propose that the emergence of these prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The ...

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A Single Adenosine with a Neutral p K _a in the Ribosomal Peptidyl Transferase Center

Cited by 246 publications

References 30 publications

Structural insights into peptide bond formation

Structural insights into peptide bond formation

Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

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A Single Adenosine with a Neutral p K a in the Ribosomal Peptidyl Transferase Center

Cited by 246 publications

References 30 publications

Structural insights into peptide bond formation

Structural insights into peptide bond formation

Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme

On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells

Contact Info

Product

Resources

About

A Single Adenosine with a Neutral p K _a in the Ribosomal Peptidyl Transferase Center