Volume 15 Issue 11, November 2008

The Fanconi anemia pathway is part of the DNA-damage network including breast cancer–susceptibility proteins BRCA1 and BRCA2. This pathway is activated by the ataxia telangiectasia and Rad3–related (ATR) kinase, but the underlying mechanism remains unclear. A new study demonstrates that a major switch activating the pathway is the ATR-dependent phosphorylation of FANCI.

The open gate of the BK-type K⁺ channel is stabilized when the voltage-sensor domains (VSDs) are activated by depolarization and the intracellular Mg²⁺ sensors are occupied. A systematic investigation reveals that each Mg²⁺ is bound by the transmembrane VSD and cytoplasmic ligand-sensing domain from two adjacent subunits, suggesting that relative positions of sensor and gate domains of BK channels may differ substantially from those suggested by homology models.

Much has been written and said about the links between the Ink4a-Arf locus, cellular senescence and stem-cell maintenance. Standing modestly in the shadows of these superstars of tumor suppression, the closely linked Ink4b gene is now emerging as a significant player in these events, and its regulation by a histone demethylase could provide new insights into how this remarkable locus is controlled.

In this issue of Nature Structural & Molecular Biology, work on the bacterial AAA+ machine ClpX provides insight into how the ATPase subunits exert a translocating force on their substrates.

The Fanconi anemia pathway is involved in the signaling of DNA damage. Several Fanconi anemia proteins have been identified, but how the pathway is actually activated was unclear. Now, work on chicken DT40 cells indicates that phosphorylation of FANCI at multiple sites triggers FANCD2 monoubiquitination and DNA-damage repair.

The bacterial AAA+ ClpX unfolds substrates using the energy from ATP hydrolysis and delivers them to the associated protease ClpP. A loop with an aromatic-hydrophobic motif protrudes into the central pore of the ClpX hexamer and was known to be important for activity. Now mutational analysis using covalently linked subunits provides evidence that this loop actually grips the substrate and undergoes conformational changes to drive its translocation and unfolding.

The voltage-sensor and RCK1 domains of BK channels act synergistically to sense electric and chemical signals. New data now indicate that the Mg²⁺-mediated interactions between these domains occurs between channel subunits, suggesting a structural arrangement that differs from other potassium channels.

The Ca²⁺ binding loops of the C₂A and C₂B domains of synaptotagmin-1 are known to be important in Ca²⁺-triggered neurotransmitter release. Biophysical and in vivo data now indicate that a basic patch on the opposite face of the C₂B domain has an equally crucial but Ca²⁺-independent role.

The Ink4a-Arf-Ink4b locus has a role in both senescence and tumorigenesis, and dysregulation can result in tumorigenesis. The Jhdm1b Jumonji family protein is now shown to be an H3K36 demethylase and is implicated in regulating cellular proliferation and senescence through p15^Ink4b.

G9a is involved in gene silencing during early embryonic development, catalyzing the methylation of H3K9, which results in heterochromatinization, and also promoting methylation of DNA de novo. These two G9a activities are now dissected, and de novo DNA methylation is shown to occur via recruitment of Dnmt3a/3b and to be necessary and sufficient to prevent reprogramming.

The antiretroviral cytidine deaminase APOBEC3G inhibits HIV-1 replication, but the enzyme is targeted for degradation by HIV-1 Vif. Protein kinase A activity is known to be elevated in HIV-1–infected T cells. New data indicate that phosphorylation of APOBEC3G by protein kinase A renders the protein less susceptible to Vif-mediated degradation.

The effect of transcription factor affinity and accessibility on gene expression has been difficult to quantify and model. The contribution of both transcription factor binding affinity and nucleosomes to tuning and diversification of gene expression output is now quantitatively uncovered, and a model that can be applied to other eukaryotic gene expression systems generated.

The spliceosome consists of five RNAs and more than 100 associated proteins. One of these, PRP8, is both one of the largest and most highly conserved spliceosomal proteins. Previous genetic and cross-linking data pointed to the importance of domain IV of PRP8 in spliceosome assembly and/or catalysis. Its structure has now been solved and found to contain an RNase H fold, suggestive of an RNA binding surface. The RNA binding data suggest that the PRP8 core recognizes, rather than a specific sequence, a structure resembling the four-helix junction proposed for the catalytically active U2/U6 snRNA interaction.

The tri-snRNP is the largest preassembled unit of the spliceosome, and its components are key to the splicing reaction. The overall structure and conformations of the yeast tri-snRNP are now analyzed by EM, and the general positions of some of its major protein components mapped.

The interferon regulatory factors (IRFs) are involved in the innate immune response and are activated by phosphorylation. The structure of a pseudophosphorylated IRF5 activation domain now reveals structural changes in the activated form that would turn an autoinhibitory region into a dimerization interface. In vivo analysis supports the relevance of such a dimer to transcriptional activation.

Group II introns are retroelements that have invaded the genomes of many prokaryotes and eukaryotes. The structure of a self-spliced group IIC intron cocrystallized with ligated exons (the target substrate) reveals the metal ions that have a role in catalysis and the intron sequences that are important in exon recognition in group II introns.

The ATPase activity of AAA+ proteins is regulated by their interaction with ligands, but depending on the particular protein it can be stimulated or inhibited, and the mechanism for such control remained unclear. An analysis of previous structural data on various AAA+ proteins now reveals that a conserved glutamate residue adopts two conformations and and thus regulates the ATPase activity.

Most known nucleotidyl-transfer enzymes use two metal ions for catalysis, but some enzymes use only one divalent cation in their active sites. A comparative analysis of previously available structural data reveals that the one-metal-ion enzymes use a similar mechanism to coordinate their single metal ion, which corresponds, functionally and structurally, to metal ion B in the two-metal-ion enzymes.