Articles in 2008

The IpaH family of Shigella virulence factors are E3 ubiquitin ligases that may target host proteins. Structural and functional characterization of IpaH1.4 and IpaH9.8 reveal a unique C-terminal catalytic domain that seems to have HECT-like E3 ligase activity. Together with an accompanying publication from Zhu et al., these data suggest that the IpaH proteins constitute a new category of ubiquitin ligases.

The IpaH proteins from Shigella show ubiquitin-ligase activity but lack obvious sequence similarity to HECT- or RING-type ubiquitin ligases. The crystal structure of IpaH3 reveals a two-domain protein with HECT-like catalytic activity mapped to a C-terminal domain of novel fold. These findings suggest that IpaH proteins represent a new family of ubiquitin ligases, a conclusion supported by results from a related study by Tyers et al.

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 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.

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 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 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 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 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 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 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.

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.

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.

DcuS is a multidomain membrane sensor kinase important for Escherichia coli interactions with its environment. A new approach combining solution- and solid-state NMR with in silico modeling and mutagenesis has provided a three-dimensional model for most of this large membrane protein and suggests a mechanism for DcuS activation.

APOBEC3G is a cytidine deaminase that can be incorporated into HIV-1 virions and process the viral genome upon cell infection, leading to viral hypermutation and inactivation. APOBEC3G's activities are counteracted by viral protein Vif. Using a sensitive enzymatic assay, low levels of APOBEC3G can be detected associated to Vif(+) virions. Furthermore, the authors show that APOBEC3G functions in a distributive manner and causes dispersed hypermutation via intersegmental transfer.

The binding of kinesin to microtubules promotes nucleotide exchange by the kinesin. Structural studies of the intermediate states of nucleotide exchange reveal the sequence of interactions and conformational changes that occur and the role of Mg²⁺ in the process, providing a testable model for microtubule-activated ADP release.

Glycine receptors (GlyR), part of the Cys-loop neurotransmitter receptor family, are Zn²⁺-modulated ion channels. Electrophysiological studies on GlyR mutants indicate that the hydrophobic cores of the channel's ligand binding domains are important for allosteric communication between the ligand-binding and Zn²⁺-inhibitory sites. The findings suggest a general activation mechanism for this receptor family.

S-adenosyl-L-methionine is a methyl donor in many biological reactions and in bacteria regulates gene expression through binding to the SAM riboswitch. The structure of a third class of SAM riboswitches now indicates which features of SAM the riboswitches have converged on to distinguish it from the closely related S-adenosyl-L-homocysteine.

In vitro, pure tubulin assembles into B-lattice microtubules, in which lateral αα and ββ contacts between tubulin heterodimers predominate. Mal3, a homolog of the plus end–tracking protein EB1, is now shown to promote microtubule assembly into an A-lattice arrangement, forcing reconsideration of in vivo microtubule structure.

Substitution of the active site gatekeeper residue in the BCR-ABL oncoprotein and related kinases is a common mechanism of imanitib resistance but has also been observed in drug-naïve patients. New work suggests that this residue stabilizes a hydrophobic spine that links the N and C kinase lobes, promoting the active conformation, and that adverse mutations at the gatekeeper residue further stabilize the spine. Disruption of the spine would be an attractive new goal in drug development.