Volume 19 Issue 2, February 2012

The Cbl family of RING finger ubiquitin ligases regulates signaling in many systems. Two new studies provide a structural basis for how phosphorylation of a specific tyrosine in the Cbl proteins enhances their ubiquitin ligase activity, giving insight into how ubiquitination by Cbl proteins is restricted to specific substrates.

A complex of PUF (named after founding members Pumilio and Fem-3 binding factor) and Argonaute proteins can stall translation elongation on bound mRNAs by interacting with eEF1A and inhibiting its GTPase activity.

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.

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.

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.

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.

The Fanconi anemia pathway is involved in the repair of DNA interstrand cross-links, but it is also involved in regulation of translesion synthesis (TLS). The protein FAAP20 is now identified as a subunit of the Fanconi anemia core complex. FAAP20 interacts with TLS DNA polymerase Rev1, stabilizing Rev1's association with PCNA and promoting DNA damage bypass.

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.

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.

Cbl RING ubiquitin ligases regulate receptor tyrosine kinase signal transduction and are in turn regulated by phosphorylation in their linker helix regions. Structural and biochemical analysis now shows that phosphorylation of c-Cbl leads to the release of an autoinhibited conformation, enhancing E2 binding and promoting ubiquitination activity.

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.

RNF8 and RNF168 are E3 ligases that promote the ubiquitination of histones at sites of double-strand breaks. Now RNF8 is shown to form mainly Lys48-linked ubiquitin chains and to modify KU80 bound to DNA breaks, promoting its removal and completion of DNA repair by NHEJ.

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.

Recent studies have called into question the extent to which crystal structures of LeuT solubilized in β-OG detergent micelles reflect functionally relevant states. Now crystal structures of LeuT in lipid bicelles—a more native membrane-like context—show LeuT–substrate complexes nearly identical to the previously reported ones, with a single substrate molecule in the primary binding site.

The splicing factor SRSF1 is an oncoprotein that is upregulated in human tumors, including breast cancer tumors. New in vitro and in vivo analyses reveal SRSF1's ability to transform human mammary epithelial cells and promote mammary gland tumorigenesis in a mouse model by regulating apoptosis and proliferation and cooperating with Myc while also uncovering potential downstream therapeutic targets.

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.

Quinol-dependent nitric oxide reductase (qNOR) catalyzes the reduction of nitric oxide, which is emitted by bacteria, to produce nitrous oxide—an ozone-depleting gas and potent greenhouse gas. The crystal structure of qNOR from Geobacillus stearothermophilus allows a structural comparison with other respiratory enzymes, revealing functionally important similarities and differences between anaerobic and aerobic respiration.

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.

Non-nucleoside inhibitors (NNRTIs) against HIV-1 reverse transcriptase (RT) are used clinically, but the mechanism by which they interfere with RT's activity is still unclear. The crystal structure of a ternary complex composed of RT, primer-template DNA and NNRTI nevirapine now reveals that binding of the drug shifts the primer 3′ end from the active site, preventing nucleotide incorporation.

Nuclear chromodomain-containing proteins read the epigenetic code by recognizing methylated lysine residues in histone tails. Structural analysis of the cytoplasmic chloroplast signal recognition particle subunit cpSRP34 in complex with the cpSRP54 subunit C-terminal tail comprising an arginine-rich motif reveals that a twinned aromatic cage reads two neighboring nonmethylated arginine residues and adapts chromodomains to a function outside the nucleus.