Brief Communications in 2013

Using embryonic stem cells as a model system for studying the basic bimodal DNA methylation pattern in vivo, a new study now indicates that demethylation is not required for generating unmethylated regions such as CpG islands as part of the overall bimodal methylation pattern but is involved in resetting methylation patterns during somatic-cell reprogramming.

The outer-membrane protein TamA is involved in autotransporter biogenesis in Escherichia coli. The crystal structure of TamA, determined to 2.3 Å, reveals a 16-strand β-barrel that is closed by a lid on its extracellular face. A weakened lateral wall in the barrel suggests the presence of a gate for substrate exit to the lipid bilayer.

Archaeal glutamate transporter homologs catalyze the coupled uptake of aspartate and sodium ions. A new crystal structure of Glt_Tk from Thermococcus kodakarensis shows the empty transporter oriented in the outward-facing conformation after substrate delivery, revealing how it is reset in preparation for another translocation cycle.

Equivalent mutations in the pseudokinase domain of Jak2 (V617F) and Jak1 (V658F) result in myeloproliferative disorders. Crystal structures of wild-type and the V658F mutant of human Jak1 spanning the pseudokinase domain and a segment of the SH2-PK linker now reveal the existence of a conformational switch that is stabilized by oncogenic mutations and favors activation.

Acetylation of the Sir3 N terminus is important for transcriptional silencing in budding yeast and is thought to promote binding of the Sir3 BAH domain to the nucleosome. Structural and biochemical analyses now demonstrate that the acetylated Sir3 N terminus does not interact with the nucleosome directly but instead stabilizes a nucleosome-binding loop in the BAH domain.

N-terminal acetylation of Sir3 is essential for heterochromatin establishment and maintenance in yeast, but its mechanism of action is unknown. The crystal structure of the N-terminally acetylated BAH domain of Sir3 bound to the nucleosome core particle revealed that N-terminal acetylation stabilizes the interaction of Sir3 with the nucleosome.

Initiation factors eIF1 and eIF1A are key determinants of ribosomal scanning and initiation-codon selection during translation initiation. The structure of Tetrahymena thermophila 40S ribosome in complex with eIF1 and eIF1A reveals the conformational changes that accompany initiation-factor binding and provides new insights into the mechanism of start-codon recognition.

Centromere protein A (CENP-A) is a histone H3 variant that specifies centromere location. Their reduced height relative to canonical H3 nucleosomes suggested that CENP-A nucleosomes might be tetrameric, but new biophysical measurements of reconstituted nucleosomes show that CENP-A confers a reduction in height on octameric CENP-A nucleosomes.

The bacterial transporter XylE is a member of the major facilitator family (MFS). The structure of XylE in its partially occluded outward-facing state was recently solved. Now the same transporter is captured in different conformational states, inward open and partially occluded inward open, thus providing insights into the transport cycle of MFS transporters.

Post-translational modifications of tRNAs can alter their decoding specificity. A molecular basis for altered codon specificity is now provided by the crystal structure of the archaeal tRNA₂^Ile modified with agmatidine at the wobble cytidine residue in complex with the AUA codon on the ribosome.