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Table of Contents for this page:

  • Current Issue
  • Advanced Online Publications Articles

  • Current Issue of Nature Structural and Molecular Biology

    Nature Structural aamp; Molecular Biology - Issue - science feeds

  • Essential modifications

  • Ubiquitin and ubiquitin-like proteins have central roles in regulating cellular processes and homeostasis. This Focus examines our understanding of the ubiquitination reaction and the mechanisms by which ubiquitin and related modifications affect protein and cellular functions.

  • Ubiquitin sets the timer: impacts on aging and longevity

  • Protein homeostasis is essential for cellular function, organismal growth and viability. Damaged and aggregated proteins are turned over by two major proteolytic routes of the cellular quality-control pathways: the ubiquitin-proteasome system and autophagy. For both these pathways, ubiquitination provides the recognition signal for substrate selection. This Commentary discusses how ubiquitin-dependent proteolytic pathways are coordinated with stress- and aging-induced signals.

  • Plant ubiquitin ligases as signaling hubs

  • The past decade has witnessed an explosion in the identification of ubiquitin-ligase complexes as the missing receptors for important small-molecule hormones regulating plant growth and development. These breakthroughs were initiated by genetic approaches, with structural analysis providing mechanistic insights into how hormone perception and signaling are coupled to protein ubiquitination. Although there are still many unknowns, plants have imparted valuable lessons about the pharmacology of ubiquitin modification.

  • Ubiquitin in inflammation: the right linkage makes all the difference

  • The immune system must operate in an effective, precise and safe manner to defend against diverse pathogens while avoiding attacking the body itself and commensal bacteria. Inflammatory pathways mediated by NOD-like, Toll-like, RIG-I–like and tumor-necrosis-factor receptor families are tightly regulated by ubiquitination, especially by Lys63-linked and linear polyubiquitin chains. Here we discuss the human ubiquitin-mediated inflammatory signaling system, emphasizing the interactions and activities whose coordination ensurestimely, accurate regulation of inflammatory responses.

  • New insights into ubiquitin E3 ligase mechanism

  • Ubiquitin E3 ligases catalyze the final step of the ubiquitination cascade, promoting the transfer of ubiquitin from the E2 to the substrate target. Recent structural and biochemical studies have given insights in the catalytic mechanisms of all three E3 ligase classes, as discussed in this Review.

  • Lysine-targeting specificity in ubiquitin and ubiquitin-like modification pathways

  • Ubiquitin and ubiquitin-like (UBL) modifications occur primarily on lysine residues of target proteins to stimulate downstream signals. This Review discusses current knowledge of lysine specificity in ubiquitin and UBL targeting, with particular focus on the systems in which a detailed mechanism of modification and downstream signaling has been validated biochemically.

  • Two-way communications between ubiquitin-like modifiers and DNA

  • DNA metabolism is regulated by the ubiquitin and SUMO modifications, but DNA also influences whether and when these modifications occur. This Review describes the mutual interactions between DNA, ubiquitin and SUMO that occur in DNA-associated processes.

  • Cleaning up in the endoplasmic reticulum: ubiquitin in charge

  • The endoplasmic reticulum–associated degradation (ERAD) pathway maintains protein homeostasis in the ER by retrotranslocating unwanted proteins to the cytosol for proteasomal degradation. This Review discusses the integral role of the ubiquitin system in ERAD, highlighting how the two pathways intertwine to facilitate transport across the ER membrane.

  • Dynamic regulation of macroautophagy by distinctive ubiquitin-like proteins

  • Whereas the proteasome degrades individual proteins modified with ubiquitin chains, autophagy degrades many proteins and organelles en masse. A pair of ubiquitin-like proteins (UBLs), Atg8 and Atg12, regulate autophagy-mediated degradation in a manner completely distinct from that of ubiquitin in the proteasome pathway, as discussed in this Review.

  • The JAMM in the proteasome

  • Structures of the deubiquitinating enzyme Rpn11 of the proteasomal 19S regulatory particle reveal its role in hydrolyzing the proximal ubiquitin from a protein that is about to be degraded.

  • RPA puts the brakes on MMEJ

  • Microhomology-mediated end joining (MMEJ) is a mechanism of DNA double-strand-break repair that creates deletions and promotes other types of genome instability. New in vivo and in vitro analyses demonstrate that the heterotrimeric replication protein A (RPA) complex prevents spontaneous annealing of microhomologies, thereby preventing genome-destabilizing MMEJ.

  • Promoter melting by an alternativeσ, one base at a time

  • Housekeepingσ factors are initiation factors for the bacterial RNA polymerase at most promoters, whereas alternative σs direct focused responses to specific environmental conditions. Structural and functional analysis of an alternative σ complexed with its cognate −10 motif elucidates the mechanism for initiation of strand opening, highlighting two critical properties: why alternative σs, compared to housekeeping σs, recognize so few promoters and how their promoter-recognition strategy was diversified during evolution.

  • X-ray crystal structure of voltage-gated proton channel

  • Structural and functional analysis reveal the resting state of the voltage-gated proton channel Hv1. Comparison with structures of voltage-sensing domains from other systems, captured in the activated state, will aid in understanding the mechanism of voltage sensing.

  • Global effects of the CSR-1 RNA interference pathway on the transcriptional landscape

  • RNAi pathways inhibit gene expression at the transcriptional and post-transcriptional level. Genome-wide analyses of nascent RNA transcripts in nematodes now suggest that the CSR-1 RNAi pathway helps maintain the directionality of active transcription and propagate the distinction between transcriptionally active and silent genomic regions.

  • Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks

  • DNA double-strand breaks (DSBs) may be repaired either by homologous recombination (HR) or nonhomologous end joining (NHEJ) pathways. A new high-resolution mapping study of DSBs in human cells shows that trimethylated histone H3 K36, a marker of active chromatin, targets RAD51 to DSBs within transcribed regions to promote preferential HR-mediated repair at transcriptionally active loci.

  • Structural basis of the proinflammatory signaling complex mediated by TSLP

  • Thymic stromal lymphopoietin (TSLP) is a cytokine critical for the development of chronic inflammatory disorders including asthma and atopic dermatitis. The structure of the ternary complex formed by TSLP and its coreceptors TSLPR and the interleukin-7 receptor reveal how TSLP is able to organize receptor-receptor contacts to facilitate intracellular signaling.

  • Structural basis for pure antagonism of integrinαVβ3 by a high-affinity form of fibronectin

  • Integrins are promising targets in the treatment of conditions that range from cancer to acute coronary syndromes. However, the partial agonism exhibited by RGD ligand–based drugs can result in life-threatening complications. A new study provides the structural basis for pure antagonism by a high-affinity integrin ligand and suggests a path to the design of safer integrin inhibitors.

  • Ty3 reverse transcriptase complexed with an RNA-DNA hybrid shows structural and functional asymmetry

  • A new study reports the first structure of a retrotransposon reverse transcriptase in complex with its cognate polypurine tract RNA-DNA hybrid. In contrast to its retroviral counterparts, Ty3 reverse transcriptase forms an asymmetric homodimer that forms in the presence of substrate, with its RNase H and DNA polymerase activities likely contributed by separate subunits.

  • Human immunoglobulin E flexes between acutely bent and extended conformations

  • IgE molecules associate with the FcɛRIα receptor in an acutely bent conformation where the Cɛ2 domains fold over the Cɛ3-Cɛ4 domains. A new study demonstrates that IgE can exist in an extended conformation with a Cɛ2 domain capable of flipping from side to side, suggesting a level of structural flexibility that could functionally impact allergen recognition.

  • RPA antagonizes microhomology-mediated repair of DNA double-strand breaks

  • Resection of DNA double strand–break ends generates single strands that can spontaneously anneal to undergo mutagenic microhomology-mediated end joining (MMEJ). A combination of genetic and biophysical assays now shows that replication protein A (RPA) thwarts strand annealing by binding to the resected ends to promote Rad51 filament assembly and error-free repair by homologous recombination.

  • Mechanism of IRSp53 inhibition and combinatorial activation by Cdc42 and downstream effectors

  • IRSp53 is a BAR-domain protein under the control of Rho family GTPases and has crucial roles in processes such as cell motility and tumor invasiveness. In a new study, IRSp53 is shown to be autoinhibited and is synergistically activated by the combinatorial action of Cdc42 and the tumor-promoting factor Eps8.

  • The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity

  • 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.

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    Nature -Advance Online Publications

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    Nature Structural aamp; Molecular Biology - AOP - science feeds

  • Conformational changes required for H+/Cl− exchange mediated by a CLC transporter

  • CLC-type H+/Cl− exchangers are known to be regulated by voltage and H+ and Cl−concentrations, but their gating mechanism remains poorly understood. New data now suggest that transport by the CLCs is regulated by two gates that are functionally linked through structural rearrangements outside of the ion-transport pathway.

  • Evidence for a group II intron–like catalytic triplex in the spliceosome

  • It has long been thought that the catalytic RNAs of self-splicing group II introns and the spliceosome function by similar mechanisms. Now, a combination of genetic, cross-linking, and biochemical analyses of yeast U6 snRNA provide compelling evidence that spliceosomal RNAs form triplex structures similar to those used by group II introns to catalyze splicing.

  • Conformational dynamics of ligand-dependent alternating access in LeuT

  • LeuT is a Na+-coupled amino acid transporter that is similar in sequence and function to eukaryotic neurotransmitter/sodium symporters, which are active in reuptake of neurotransmitters from the synapse. Distance measurements between spin-label pairs are used to identify ligand-dependent structural transitions in LeuT.

  • Crystal structure of ATP-bound Get3–Get4–Get5 complex reveals regulation of Get3 by Get4

  • Tail-anchor proteins are targeted post-translationally to the endoplasmic reticulum via the conserved GET pathway, in which the Get4–Get5 complex mediates delivery of substrates to Get3, the central targeting factor. The crystal structure of the ATP-bound Get3–Get4–Get5 complex and functional analyses reveal how Get4–Get5 primes Get3 for substrate loading.

  • Kin28 regulates the transient association of Mediator with core promoters

  • The genomic localization of Mediator in budding yeast is now assessed, revealing that Mediator remains associated with upstream activating sequences until it becomes transiently associated with core promoters during initiation. Phosphorylation of the CTD of Rpb1 at Ser5 by Kin28 releases Mediator prior to elongation.

  • Mechanism of activation of bacterial cellulose synthase by cyclic di-GMP

  • Cyclic di-GMP (c-di-GMP) regulates a number of bacterial processes, including synthesis of cellulose during biofilm formation. The PilZ domain from bacterial cellulose synthase BcsA–BcsB senses c-di-GMP and activates the enzyme. Now crystal structures of BcsA–BcsB along with functional analysis reveal that binding of c-di-GMP releases a conserved gating loop to allow substrate to enter the active site.

  • Structural basis of recognition of interferon-α receptor by tyrosine kinase 2

  • How the four JAK kinases discriminate between different cytokine receptors is not well understood. The first crystal structure of a JAK kinase (TYK2) bound to a cytokine receptor (INFAR1) now exposes a multipoint interaction mode that involves an atypical phosphoindependent interaction between TYK2's SH2 domain and INFAR1's conserved box2 motif.
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