Articles in 2012

Crystal structures of the bacterial LeuT Na⁺-substrate symporter have revealed one substrate molecule in an occluded, centrally located binding site, whereas subsequent studies identified a putative second substrate binding site. Now additional binding analyses demonstrate that the second substrate binding site can be obscured during the preparation of detergent-solubilized LeuT for crystallography, explaining the apparent discrepancy in the reported stoichiometry.

The core Qβ replicase is comprised of Qβ virus–encoded RNA-dependent polymerase and bacterial host–derived EF-Tu and EF-Ts, but the functions of these translation factors in RNA polymerization have been unclear. Structural analysis of Qβ replicase during polymerization reveals that EF-Tu functions as a modulator to separate the growing RNA strand from the template, ensuring processivity of the complex.

Protease phosphorylation has been reported to affect many signaling pathways connected to proteolytic activity, but the underlying mechanisms have not been clearly elucidated. Structural and biochemical analyses of the deubiquitinase DUBA reveal that phosphorylation is necessary for productive ubiquitin substrate recognition and for enzyme activity.

HtrA proteins have chaperone and protease activities, but how they bind and fold their substrates is poorly understood. New cryo-EM analyses of a protease-defective bacterial DegQ mutant in complex with several different substrates provide a structural model of HtrA proteins in their chaperone mode.

Small noncoding RNAs function together with Argonaute (Ago) proteins as part of RNA-induced silencing complexes (RISCs). New biochemical analyses have identified the N domain of human AGO2 as the initiator of small duplex RNA unwinding during RISC assembly, which is required for both slicer-dependent and slicer-independent unwinding mechanisms.

The processivity of myosins and kinesins has been well studied, but how the dynein homodimer achieves continuous motion is unknown. Two-dimensional analysis of labeled, DNA-dimerized dynein demonstrates that dynein has an unusual stepping pattern and can alternate between stochastic- and tension-based stepping to achieve processivity.

Although the asymmetric dimethylation of histone H3R2 acts as a repressive mark, new studies reveal that symmetrically dimethylated H3R2 (H3R2me2s) is a functional histone mark in vivo. The RBBP7 co-repressor is excluded from binding H3R2me2s in favor of the coactivator WDR5, which poises euchromatic genes for transcription activation upon cell-cycle exit and differentiation.

KirBac channels are the bacterial homologs of mammalian inwardly rectifying potassium (Kir) channels. All available structures are closed at the helix bundle crossing, but the crystal structure of an open-state KirBac channel now indicates how opening of the primary activation gate may be physically coupled to a rotational twist in the cytoplasmic domain.

Eukaryotic cells choose the pathway to repair DNA double-strand breaks according to the cell-cycle phase, with homologous recombination preferred during S and G2 phases. Now the direct interaction between CDK2 and the C-terminus of Mre11 is revealed and shown to be important for phosphorylation of CtIP.

PUF (Pumilio/FBF) RNA-binding proteins and Argonaute (Ago) miRNA-binding proteins regulate mRNAs post-transcriptionally, each acting through similar yet distinct mechanisms. New genetic and biochemical analyses demonstrate that PUF and Ago proteins also function together in complex with elongation factor eEF1A to repress translation elongation.