Articles in 2010

The anthrax lethal toxin protein transporter consists of protective antigen (PA) and lethal factor (LF), with LF unfolding for translocation into the host cell. Structural and functional analyses now indicate how each of four LFs unfolds and binds into amphipathic clefts on the surface of the PA octomer.

Open channel blockers are very different in their chemistry and structure. Now GLIC, a bacterial model for pentameric ligand-gated channels, is used to investigate the structural basis of open channel block. The work identifies two extended interaction sites, with large blockers binding to the center of the membrane and small blockers binding to the narrow intracellular region.

A genome-wide analysis of replication profiles in different budding yeast mutants reveals that the alternative clamp loader component Ctf18 has a key role in the DNA replication checkpoint, acting together with Mrc1 to promote Rad53 phosphorylation.

Notch signaling regulates key developmental events, and aberrant Notch signaling has been linked to disease. The structure of a dimeric Notch transcription complex with DNA is presented, revealing how dimer-binding sites with different spacers may be recognized. Cryptic dimer-binding sites are also uncovered, which might account for differential sensitivity of promoters to cooperative assembly of complexes.

Vesicle tethering is the least well understood step of vesicular transport. The core conserved oligomeric Golgi (COG) vesicle tethering complex from yeast, consisting of the four essential subunits Cog1–4, is now reconstituted and characterized by negative stain EM and single particle analysis. The COG complex forms a y-shaped structure, whose central region and the distal regions of at least two legs all participate in interactions with other components of the intracellular trafficking machinery.

How a variety of nuclear export signals (NESs) are recognized by their receptor CRM1 is now examined by crystallography, NMR spectroscopy, biochemistry and cellular approaches. The work reveals that the different NES peptides adopt different conformations to fit into five rigid hydrophobic binding pockets on CRM1, and redefines an NES consensus.

Alternative splicing can be affected by transcription elongation rate and genotoxic stress. Camptothecin is now shown to induce MDM2 exon skipping in a p53-independent and reversible manner. This process involves disrupting EWS and YB-1 interaction, which are Pol II and spliceosome-associated factors, respectively.

Yeast possesses eight multisubunit vesicle tethering complexes, including TRAPPI and TRAPPII. The TRAPPII complex functions in the late Golgi and consists of all TRAPPI and three specific subunits. Purified native yeast TRAPPII is now characterized by single-particle electron microscopy, providing insights into the molecular basis for human pathologies resulting from defective TRAPP complex function.

The prokaryotic ubiquitin-like protein Pup is involved in the Mycobacterium tuberculosis proteasome pathway but is an intrinsically disordered protein, unlike eukaryotic Ub. Structural data now indicate that the Mycobacterium proteasomal ATPase (Mpa) binds Pup in an α-helical form, indicative of binding-induced folding of Pup upon reaching the proteasome in this system.

Understanding the genesis of histone may give functional insight and elucidate maintenance of post-translational histone modifications. Using biochemical purification and characterization from human cell fractions, the authors examine pre-deposition histone complexes, giving insight into processes from assembly through to nuclear import.

Nuclear HIV-1 mRNA export is mediated by cooperative Rev protein binding to the Rev response element (RRE) RNA, forming a complex recognized by the Crm1 host export factor. A structure of a Rev dimer now shows that the organization of Rev monomers within a dimer defines the RRE recognition interface, with the other side likely binding Crm1.

The crystal structure of the complex formed by the death domains from Fas and FADD at physiological pH is now solved, revealing a 5:5 complex that is supported by electron microscopy data. Along with mutagenesis and mass spectrometry analyses, the work provide insight into Fas mutations that cause autoimmune lymphoproliferative syndrome.

Electron cryo-microscopy images of actin filaments (F-actin) allow the visualization of different conformational states, which can be classified into different groups. Further analyses reveal the plasticity of the subdomain 2 region and suggest that missense mutations related to disease affect F-actin structural dynamics.

A complex substrate containing mobile double Holliday junctions is now used to show that yeast proteins Sgs1 (DNA helicase) and Top3 (topoisomerase) act together to dissolve the junctions and avoid crossing over; the protein Rmi1 stimulates this process.

Rad51 plays a central role in homologous recombination pathways. Now work with Xenopus laevis egg extracts shows that Rad51 prevents formation of DNA gaps at or behind replication forks, which are dependent on Mre11 nuclease activity.

The N-end rule pathway is a proteolytic system in which recognition components (N-recognins) recognize a set of N-terminal residues as part of degradation signals (N-degrons). Two studies in this issue report the structures of Ubr boxes, a substrate recognition domain of eukaryotic N-recognins. We discuss how eukaryotic and prokaryotic N-recognins use a similar molecular principle to recognize a different set of N-degrons.

In this issue, Wu et al. show that the RecBC helicase, which is involved in repairing double-strand DNA breaks, uses one ATPase motor to drive two translocases along opposite strands of DNA—much as an all-wheel drive engine controls movement of both front and back wheels. This mechanism may allow RecBC to load onto blunt-end DNA more efficiently and to move through obstacles such as gaps and DNA damage.

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