Phospholipases A2 hydrolyze stereospecifically the acyl ester in position 2 of 3-sn-phosphatidyl derivatives.The most intriguing characteristic of these enzymes is their ability to recognize the state of aggregation of the substrate (see e.g.Refs. 1 and 2).A variety of hypotheses had been advanced to account for this unusual enzymatic specificity (see e.g.Ref.
AbstractThe pseudouridine synthase (Ψ synthase) TruA catalyzes the conversion of uridine to pseudouridine at positions 38, 39, and/or 40 in the anticodon stem-loop (ASL) of tRNA. We have determined the crystal structure of TruA from Thermus thermophilus HB8 at 2.25 Å resolution. TruA and the other Ψ synthases have a completely conserved active site aspartate, which suggests that the members of this enzyme family share a common catalytic mechanism. The T. thermophilus TruA structure reveals the remarkably flexible structural features in the tRNA-binding cleft, which may be responsible for the primary tRNA interaction. In addition, the charged residues occupying the intermediate positions in the cleft may lead the tRNA to the active site for catalysis. Based on the TruB-tRNA complex structure, the T. thermophilus TruA structure reveals that the tRNA probably makes the melting base pairs move into the cleft, and suggests that a conformational change of the substrate tRNA is necessary to facilitate access to the active site aspartate residue, deep within the cleft.
The concave surface of the crescent-shaped Bin-amphiphysin-Rvs (BAR) domain is postulated to bind to the cell membrane to induce membrane deformation of a specific curvature. The Rac binding (RCB) domain/IRSp53-MIM homology domain (IMD) has a dimeric structure that is similar to the structure of the BAR domain; however, the RCB domain/IMD has a "zeppelin-shaped" dimer. Interestingly, the RCB domain/IMD of IRSp53 possesses Rac binding, membrane binding, and actin filament binding abilities. Here we report that the RCB domain/IMD of IRSp53 induces membrane deformation independent of the actin filaments in a Rac-dependent manner. In contrast to the BAR domain, the RCB domain/IMD did not cause long tubulation of the artificial liposomes; however, the Rac binding domain caused the formation of small buds on the liposomal surface. When expressed in cells, the Rac binding domain induced outward protrusion of the plasma membrane in a direction opposite to that induced by the BAR domain. Mapping of the amino acids responsible for membrane deformation suggests that the convex surface of the Rac binding domain binds to the membrane in a Rac-dependent manner, which may explain the mechanism of the membrane deformation induced by the RCB domain/IMD.
Helimagnetic materials are identified as promising for novel spintronic applications. Since helical spin order is manifested as a compromise of competing magnetic exchange interactions, its emergence is limited by unique constraints imposed by the crystalline lattice and the interaction geometries as exemplified by the multiferroic perovskite manganites with large orthorhombic distortion. Here we show that a simple cubic perovskite ${\mathrm{SrCoO}}_{3}$ with room-temperature ferromagnetism has the potential to host helimagnetic order upon isotropic lattice expansion. Increasing the Ba content $x$ in ${\mathrm{Sr}}_{1\ensuremath{-}x}{\mathrm{Ba}}_{x}{\mathrm{CoO}}_{3}$ continuously expands the cubic lattice, eventually suppressing the ferromagnetic order near $x=0.4$ where helimagnetic correlations are observed as incommensurate diffuse magnetic scattering by neutron-diffraction measurements. The emergence of helimagnetism is semiquantitatively reproduced by first-principles calculations, leading to the conjecture that a simple cubic lattice with strong $d\text{\ensuremath{-}}p$ hybridization can exhibit a variety of novel magnetic phases originating from competing exchange interactions.
Abstract ‘RNA recognition motifs (RRMs)’ are common domain‐folds composed of 80–90 amino‐acid residues in eukaryotes, and have been identified in many cellular proteins. At first they were known as RNA binding domains. Through discoveries over the past 20 years, however, the RRMs have been shown to exhibit versatile molecular recognition activities and to behave as molecular Lego building blocks to construct biological systems. Novel RNA/protein recognition modes by RRMs are being identified, and more information about the molecular recognition by RRMs is becoming available. These RNA/protein recognition modes are strongly correlated with their biological significance. In this review, we would like to survey the recent progress on these versatile molecular recognition modules. WIREs RNA 2012, 3:229–246. doi: 10.1002/wrna.1107 This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein–RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA–Protein Complexes
Abstract Post‐transcriptional modifications of bases within the transfer RNAs (tRNA) anticodon significantly affect the decoding system. In bacteria and eukaryotes, uridines at the wobble position (U34) of some tRNAs are modified to 5‐methyluridine derivatives (xm 5 U). These xm 5 U34‐containing tRNAs read codons ending with A or G, whereas tRNAs with the unmodified U34 are able to read all four synonymous codons of a family box. In Escherichia coli ( E.coli ), the bifunctional enzyme MnmC catalyzes the two consecutive reactions that convert 5‐carboxymethylaminomethyl uridine (cmnm 5 U) to 5‐methylaminomethyl uridine (mnm 5 U). The C‐terminal domain of MnmC (MnmC1) is responsible for the flavin adenine dinucleotide (FAD)‐dependent deacetylation of cmnm 5 U to 5‐aminomethyl uridine (nm 5 U), whereas the N‐terminal domain (MnmC2) catalyzes the subsequent S ‐adenosyl‐L‐methionine‐dependent methylation of nm 5 U, leading to the final product, mnm 5 U34. Here, we determined the crystal structure of E.coli MnmC containing FAD, at 3.0 Å resolution. The structure of the MnmC1 domain can be classified in the FAD‐dependent glutathione reductase 2 structural family, including the glycine oxidase ThiO, whereas the MnmC2 domain adopts the canonical class I methyltransferase fold. A structural comparison with ThiO revealed the residues that may be involved in cmnm 5 U recognition, supporting previous mutational analyses. The catalytic sites of the two reactions are both surrounded by conserved basic residues for possible anticodon binding, and are located far away from each other, on opposite sides of the protein. These results suggest that, although the MnmC1 and MnmC2 domains are physically linked, they could catalyze the two consecutive reactions in a rather independent manner.
