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Type I restriction-modification enzymes recognize a target sequence and translocate DNA from both sides while remaining stationary, creating supercoiled loops and cleaving at nonspecific sites several kilobases away. The crystal structure of the motor subunit of EcoR124I is now solved, providing insight into these complex machines.
Plants contain atypical RNA polymerases that have been implicated in RNA silencing. An analysis of RNA polymerase V composition now reveals that it unexpectedly shares some, but not all, subunits found in RNA polymerase II, indicating that it may be a derived version of this polymerase complex. Additional subunits are also identified and implicated in RNA-mediated silencing.
TIPE2 is involved in immune homeostasis, and it has been assumed that it contained a death effector domain (DED). Now the crystal structure of TIPE2 reveals that it does not possess a DED, but instead has a previously uncharacterized fold, with a large central cavity that might accommodate a ligand.
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.
Kinesins are molecular motors that slide along microtubules. A quantum dot is now attached to a microtubule, allowing the visualization of its rotation as it is moved by kinesins. The rotational pitch provides information about the motor, revealing the low processivity of human mitotic kinesin Eg5.
Histone methylation has important consequences for chromatin activity. Now, histones with methyllysine analogs are used to reconstitute nucleosomes: the crystal structures show no global changes in nucleosomes with H3K79me2 and H4K20me3, but the latter modification enhances compaction of nucleosomal arrays.
Repeat-addition processivity (RAP), that is, generating multiple DNA repeats from a single template without primer dissociation, is a key property of telomerase. In the Tetrahymena reverse-transcriptase component of telomerase, a single amino acid mutation causes a profound and specific defect in RAP without altering enzymatic activity.
The NMR structure of the H2A.Z-H2B histone chaperone, Chz1, reveals electrostatic interactions between Chz1 and the histone pair via a long, irregular chain with two capping helices, and, based on a model, the possibility that Chz1 has a more active role in histone replacement is suggested.
PPARγ is a nuclear receptor that regulates metabolic homeostasis. It is activated by nitrated and oxidized fatty acids. The crystal structure of the ligand binding domain of PPARγ in complex with a physiological ligand, nitrated linoleic acid, is now described, showing differences with synthetic agonists that may have physiological relevance.
Toll-like receptor 3 (TLR3) recognizes double-stranded RNA (dsRNA) molecules produced by many viruses and activates an inflammatory response. Synthetic dsRNAs such as small interfering RNAs have been shown to activate TLR3. Now the TLR3 ectodomain is found to contain two dsRNA binding sites, and the implications for dsRNA recognition and selectivity and downstream signaling are discussed.
Cytoplasmic O-GlcNac modification of proteins is thought to have dynamic interplay with phosphorylation and thus be involved in regulation of signaling processes. The complete structure of an OGT homolog is now presented, suggesting how diverse ligands can be presented to the active site of the enzyme.