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Ubiquitin-like protein (Ubl)-specific proteases catalyze Ubl precursor processing and deconjugation. Two recent structural studies of SUMO-specific protease (SENP)–substrate complexes provide new insight into hydrolysis of the peptide bond at the C terminus of SUMO. A kinked, cis configuration for the scissile bond is crucial for proteolysis.
The mechanism by which ATP-dependent remodeling enzymes act to space nucleosomes is as yet unclear. A new study uses FRET to monitor nucleosome repositioning in real time to address how these enzymes sense when nucleosomes are evenly distributed.
The first structures of an intramembrane serine protease reveal a catalytic His-Ser dyad in a water-filled cavity surrounded by six transmembrane helices, but just how substrate helices gain access to the dyad is controversial.
Crystal structures of T4 RNA ligase 2 trapped at different stages of a multistep reaction show how one enzyme active site juggles three phosphoryl transfer reactions to join two RNA strands. The structures also show how the ligase enzyme selectively recognizes the sugar pucker of ribose to achieve catalytic specificity toward RNA-containing substrates.
Recent additions to the helicase family include motor proteins that do not actually unwind DNA, but rather translocate it. By sensing short polar sequences that orient the bacterial chromosome, the FtsK helicase translocates DNA so as to align the termini of replicated chromosomes with each other, facilitating the late stages of chromosome segregation.
Recent data suggest that the C-terminal domain of RNA polymerase II can repress exon inclusion via a mechanism not explained by the prevailing models for cotranscriptional splicing regulation.
The DEAD-box ATPase Ded1 unwinds duplex RNA with a single-stranded overhang; however, Ded1 requires the overhang not for translocation but rather for loading onto the duplex. This surprising finding expands the mechanistic repertoire for the ubiquitous DExD/H-box family.
Eukaryotic transcriptomes are considerably larger than estimated from simple gene counts. However, much of this 'excess' RNA is immediately cleared from cells. Two recent studies reveal that so-called cryptic unstable transcripts constitutively transcribed from the yeast genome are rapidly eliminated in a process that couples transcription termination to RNA degradation.
Many translation initiation inhibitors block transfer RNA binding or placement in the ribosome. Structures of kasugamycin bound to the bacterial ribosome now indicate that it instead blocks proper mRNA placement.
The structure of the ligand-binding domains of Vibrio harveyi LuxPQ bound to Autoinducer-2 reveals a dramatic asymmetry in quaternary structure induced by ligand binding. Structures of receptor-sensing domains in both occupied and unoccupied states provide a foundation for postulating mechanisms of transmembrane signaling.
MicroRNAs (miRNAs) are noncoding small RNAs thought to post-transcriptionally regulate many metazoan genes by binding to partially complementary sites in target messenger RNAs. In this issue, Didiano and Hobert examine known and predicted targets of the nematode lsy-6 miRNA, question the general validity of previously proposed rules about miRNA-target interactions and suggest that many functional miRNA targets might be context dependent, as seen in metazoan gene regulation by transcription factors.
The activation-deactivation cycles of G proteins underlie their key roles as molecular switches for a vast array of biological responses. A study in this issue obtains a first look at how G protein–coupled receptors activate heterotrimeric G proteins to switch on signaling pathways by inducing a specific conformational change within their α subunits.
The structure of Escherichia coli RNase II is the first in the broadly conserved RNB family of exoribonucleases. It explains the catalytic properties of RNase II itself and provides insight into an important eukaryotic RNA degradation and processing complex, the exosome.