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A new crystal structure of BtuCD, a bacterial ABC transporter that uses ATP hydrolysis to drive vitamin B12 uptake, bound to an AMP-PNP nucleotide, completes the structural elucidation of intermediates in the transport cycle and reveals how ATP accelerates transport.
An X-ray crystal structure of substrate-bound Neisseria PnuC, a bacterial member of the SWEET family of transporters, provides key insights into the translocation mechanism and potential evolution of these membrane proteins.
PRC2 promotes methylation of H3K27, a modification that recruits PRC1, which in turn deposits H2A ubiquitin marks. Müller and colleagues use biochemistry approaches to show that H2Aub recruits Jarid–Aebp2–containing PRC2 to promote H3K27 trimethylation on H2Aub nucleosomes, thus forming a positive feedback loop to establish repressed chromatin domains.
5'-adenylated DNA adducts generated during nucleotide excision repair (NER) are removed by aprataxin to permit DNA end ligation. Now, structural and kinetic analyses reveal that NER enzymes DNA polymerase β and FEN1 can also excise these adducts and thus provide a 'backup' repair pathway for abasic sites.
Human endogenous retrovirus subfamily H (HERVH) is a class of transposable elements expressed preferentially in human embryonic stem cells (hESCs). A new study now shows that the long terminal repeats of HERVH function as enhancers and that HERVH is a nuclear long noncoding RNA required to maintain hESC identity.
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 GltTk 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 tRNA2Ile modified with agmatidine at the wobble cytidine residue in complex with the AUA codon on the ribosome.
Adenosylcobalamin is a form of vitamin B12 that serves as a coenzyme in different reactions and as a ligand for riboswitches to control bacterial gene expression. The crystal structure of a B12 riboswitch from Symbiobacterium thermophilum bound to its ligand adenosylcobalamin is now presented, revealing the determinants for ligand recognition and gene expression control.
A systematic in vitro analysis of five different forms of cytosine in mammalian and yeast RNA polymerase II (Pol II) transcription demonstrates that Pol II can read and distinguish subtle differences in modified cytosines and process them differently, suggesting a putative functional interplay between cytosine modification status and transcription.
The assembly of diverse immunoglobulin genes results in part from Rag protein–mediated DNA double-strand breaks at the edges of immunoglobulin gene segments, followed by the combinatorial reassembly of these segments. A transposase from the insect Helicoverpa zea is now shown to be active in vitro, and its breakage and joining activities resemble those of Rag, suggesting a common progenitor.
STING is an important component of the innate immune system involved in the direct response to the bacterial second messenger c-di-GMP. The structures of human STING in the presence and absence of c-di-GMP show how recognition of c-di-GMP is achieved by dimeric STING, providing a basis for future studies investigating signal transduction mechanisms.
The crystal structures of human STING in the apo and c-di-GMP–bound states, supported by mutagenesis and biochemical data, reveal that c-di-GMP binds to preformed dimeric STING. c-di-GMP prolongs STING phosphorylation in vitro, which may contribute to downstream IFN signaling. These findings aid in understanding the innate immune response to bacterial infection.