Crystal Structures of <i>Acetobacter aceti</i> Succinyl-Coenzyme A (CoA):Acetate CoA-Transferase Reveal Specificity Determinants and Illustrate the Mechanism Used by Class I CoA-Transferases

Coenzyme A (CoA)-transferases catalyze transthioesterification reactions involving acyl-CoA substrates, using an active-site carboxylate to form covalent acyl anhydride and CoA thioester adducts. Mechanistic studies of class I CoA-transferases suggested that acyl-CoA binding energy is used to accelerate rate-limiting acyl transfers by compressing the substrate thioester tightly against the catalytic glutamate [White, H., and Jencks, W. P. (1976) <i>J. Biol. Chem. 251</i>, 1688–1699]. The class I CoA-transferase succinyl-CoA:acetate CoA-transferase is an acetic acid resistance factor (AarC) with a role in a variant citric acid cycle in <i>Acetobacter aceti</i>. In an effort to identify residues involved in substrate recognition, X-ray crystal structures of a C-terminally His₆-tagged form (AarCH6) were determined for several wild-type and mutant complexes, including freeze-trapped acetylglutamyl anhydride and glutamyl-CoA thioester adducts. The latter shows the acetate product bound to an auxiliary site that is required for efficient carboxylate substrate recognition. A mutant in which the catalytic glutamate was changed to an alanine crystallized in a closed complex containing dethiaacetyl-CoA, which adopts an unusual curled conformation. A model of the acetyl-CoA Michaelis complex demonstrates the compression anticipated four decades ago by Jencks and reveals that the nucleophilic glutamate is held at a near-ideal angle for attack as the thioester oxygen is forced into an oxyanion hole composed of Gly388 NH and CoA N2″. CoA is nearly immobile along its entire length during all stages of the enzyme reaction. Spatial and sequence conservation of key residues indicates that this mechanism is general among class I CoA-transferases

Shocks de Precios Relativos e Inflación: La Mediana Ponderada como Medida de Inflación Subyacente en Chile

Relative price shocks with zero mean can affect measured inflation in the presence of non-convex adjustment costs, if core inflation is different from zero or the distribution of the shock is asymetric. In such cases, central tendency measures of the shock's distribution are a better measure of core inflation. The purpose of this paper is to calculate and evaluate the properties of the weighted median as an indicator of core inflation in Chile. This paper analyzes the cross sectional distribution of price changes in Chile. It is shown that this distribution is very asymmetric, and that the degree of asymmetry is an important explanatory variable of actual inflation. In comparison to CPI and more traditional measures of core inflation, the weighted median is more correlated to past innovations in monetary aggregates, and constitutes a better predictor of future inflation.

ACOCT primes the oxalate-induced ATR cycle.

<p>YfdW and YfdU appear to be required for the oxalate-induced ATR <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Fontenot1" target="_blank">[19]</a>. Arrows indicate the expected physiological direction; only OXC catalyzes an irreversible reaction <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Svedrui1" target="_blank">[13]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Maeda1" target="_blank">[73]</a>. ACOCT enables the synthesis of oxalyl-CoA when formyl-CoA and formate are unavailable (e.g., aerobic conditions). The aerobic fate of formate is unclear; the FHL reaction in the dotted box is associated with anaerobic conditions. Oxalate/formate antiport is not detected in <i>E. coli </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Fontenot1" target="_blank">[19]</a>. ACOCT and FCOCT could also work together to support the oxalate-catalyzed interconversion of formyl-CoA/acetate and acetyl-CoA/formate (not shown).</p

HPLC analysis of ACOCT reaction progress.

<p>HPLC traces showing time-dependent conversion of acetyl-CoA to oxalyl-CoA by UctC. IsoCoA is the -phosphoryl isomer of CoA <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Burns1" target="_blank">[49]</a>. Black trace, ; red trace, min; blue trace, min.</p

Stereogram of FCOCT and ACOCT active sites.

<p>Superposition of H6YfdE structure (gray, PDB entry 4hl6) on several <i>O. formigenes</i> FRC structures: apo (green, PDB entry 1p5h) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Ricagno1" target="_blank">[69]</a>, aspartylformyl anhydride adduct plus CoA (light brown, PDB entry 2vjm) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Berthold1" target="_blank">[20]</a>, and aspartyl-CoA thioester adduct plus oxalate (purple, PDB entry 2vjo) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Berthold1" target="_blank">[20]</a>. Bold italic letters identify significant features in the H6YfdE active site.</p

Class III CoA-transferases associated with oxalate metabolism.

<p>Selected gene clusters that contain <i>oxc</i> (white backgrounds) and two class III CoA-transferase genes. CoA-transferase gene names are shown in white: black backgrounds, FCOCT subgroup; medium-gray backgrounds, ACOCT subgroup. UniProt accession numbers are given for each CoA-transferase. Unrelated proteins have light gray backgrounds; flanking proteins on the opposite DNA strands are not shown, except for the end of the <i>E. coli evgS</i> gene, the sensor kinase of the EvgAS two-component response regulator <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Masuda1" target="_blank">[14]</a>. Stars indicate the locations of inverted repeats to which EvgA binds, inducing the expression of <i>yfdX</i> and <i>yfdWUVE </i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901-Masuda2" target="_blank">[15]</a>.</p

Stereogram of the H6YfdE dimer.

<p>One subunit is shown as a rainbow-colored cartoon where the color gradient corresponds to the sequence; the small domain is at the bottom. The other subunit is shown as a light gray ribbon. Small spheres and numbers identify the -carbon at intervals of 20 residues. The active site residues Asp173 and His233 (large spheres) are provided by different subunits in each active site. A topology diagram is provided in the Supporting Information (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0067901#pone.0067901.s005" target="_blank">Figure S5</a>). (A) View with the pseudo-twofold axis relating the subunits vertical in the plane of the page. Spheres corresponding to residues 220 and 240 are hidden by the partner subunit. (B) View along the long axis of one subunit as indicated by the large arrow in panel A.</p

A New Family of HEAT-Like Repeat Proteins Lacking a Critical Substrate Recognition Motif Present in Related DNA Glycosylases

<div><p>DNA glycosylases are important repair enzymes that eliminate a diverse array of aberrant nucleobases from the genomes of all organisms. Individual bacterial species often contain multiple paralogs of a particular glycosylase, yet the molecular and functional distinctions between these paralogs are not well understood. The recently discovered HEAT-like repeat (HLR) DNA glycosylases are distributed across all domains of life and are distinct in their specificity for cationic alkylpurines and mechanism of damage recognition. Here, we describe a number of phylogenetically diverse bacterial species with two orthologs of the HLR DNA glycosylase AlkD. One ortholog, which we designate AlkD2, is substantially less conserved. The crystal structure of <i>Streptococcus mutans</i> AlkD2 is remarkably similar to AlkD but lacks the only helix present in AlkD that penetrates the DNA minor groove. We show that AlkD2 possesses only weak DNA binding affinity and lacks alkylpurine excision activity. Mutational analysis of residues along this DNA binding helix in AlkD substantially reduced binding affinity for damaged DNA, for the first time revealing the importance of this structural motif for damage recognition by HLR glycosylases.</p></div