Nature Structural & Molecular Biology Contents: 2015 Volume #22 pp 647-750

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TABLE OF CONTENTS September 2015 Volume 22, Issue 9 News and Views Perspective Articles Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement Nature Microbiology: Call for Papers Launching in January 2016, Nature Microbiology is now open for submissions and inviting high-quality submissions. The journal will cover all aspects of microorganisms be it their evolution, physiology and cell biology, their interactions with each other, with a host, with an environment, or their societal significance.  Submit your next research paper to the journal.     News and Views Top Plasmepsin V shows its carnivorous side   pp647 - 648 Daniel E Goldberg doi:10.1038/nsmb.3077 Export of effector proteins is crucial for the virulence program of the malaria parasite Plasmodium falciparum. A crystal structure of the P. falciparum processing enzyme essential for protein export reveals noncanonical aspartic protease features and provides an avenue for antimalarial drug development. Want reprogramming? Cut back on the chromatin assembly!   pp648 - 650 Paul D Kaufman doi:10.1038/nsmb.3081 Totipotency, the ability of early embryonic cells to generate a complete adult organism as well as extraembryonic tissue, is a fleeting property found only in very early embryonic cells. A breakthrough study now shows that inhibition of DNA replication-linked nucleosome assembly causes embryonic stem cells to resemble totipotent cells. Notably, inhibition of chromatin assembly stimulates reprogramming during somatic-cell nuclear transfer experiments. See also: Article by Ishiuchi et al. PsbS is the plants' pick for sun protection   pp650 - 652 Roberta Croce doi:10.1038/nsmb.3079 Plants protect themselves from fluctuating high-light conditions by dissipating a large part of their absorbed energy as heat, in a process that requires the protein PsbS. The structure of PsbS opens new possibilities for understanding the mechanism of photoprotection in plants. See also: Article by Fan et al. A timer to coordinate substrate processing by the 26S proteasome   pp652 - 653 Tingting Yao doi:10.1038/nsmb.3085 The eukaryotic 26S proteasome is responsible for degrading virtually any protein with an appropriate ubiquitin signal, and in the process ubiquitin is spared and recycled. Two studies of the proteasome-associated deubiquitinase UBP6 now shed light on how deubiquitination coordinates the cycle of substrate processing. See also: Article by Bashore et al. SMC condensin: promoting cohesion of replicon arms   pp653 - 655 Frank Burmann & Stephan Gruber doi:10.1038/nsmb.3082 Two studies using chromosome conformation capture (3C) analyses in the Gram-positive bacterium Bacillus subtilis have revealed a global pattern of chromosome organization that originates from loading sites of the Smc-ScpAB complex. Loading Smc-ScpAB at a single genomic location is sufficient to promote genome-wide folding of DNA into a well-defined structure. PAR and the organization of the DNA damage response   p655 Inês Chen doi:10.1038/nsmb.3089 Structural & Molecular Biology JOBS of the week Post-Doctoral / Senior Research Northwestern University Assistant / Associate Professor University of Colorado Anschutz Medical Campus Postdoctoral Position - Postdoctoral Fellow The University of Tennessee Health Science Center For Junior, Tenure-Track Faculty University of Michigan More Science jobs from Structural & Molecular Biology EVENT IWBE-2015, 2nd International Workshop on Biomedical Engineering and Bioinformatics 07.11.15 Istanbul, Turkey More science events from Perspective Top Charting oxidized methylcytosines at base resolution   pp656 - 661 Hasan Yardimci and Yi Zhang doi:10.1038/nsmb.3071 New methods permit genomic mapping of oxidized methylcytosines at single-base resolution and suggest new regulatory functions for 5-methylcytocine (5mC) derivatives 5hmC, 5fC and 5caC in the mammalian genome. Articles Top Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly   pp662 - 671 Takashi Ishiuchi, Rocio Enriquez-Gasca, Eiji Mizutani, Ana Bošković, Celine Ziegler-Birling,Diego Rodriguez-Terrones, Teruhiko Wakayama, Juan M Vaquerizas & Maria-Elena Torres-Padilla doi:10.1038/nsmb.3066 New data show that depletion of histone chaperone CAF-1 in mouse embryonic stem (ES) cells induces early embryonic-like cells that exhibit gene-expression patterns and reprogramming efficiencies characteristic of 2-cell-stage populations that arise spontaneously in ES-cell culture, thus suggesting that altered chromatin assembly contributes to differences in stem-cell plasticity. See also: News and Views by Kaufman The tuberculosis necrotizing toxin kills macrophages by hydrolyzing NAD   pp672 - 678 Jim Sun, Axel Siroy, Ravi K Lokareddy, Alexander Speer, Kathryn S Doornbos,Gino Cingolani & Michael Niederweis doi:10.1038/nsmb.3064 The Mycobacterium tuberculosis necrotizing toxin (TNT) is shown to cause toxicity by hydrolyzing NAD+ in the host cell. The crystal structure of TNT bound to its immunity factor reveals a new NAD+ glycohydrolase fold. Recognition of the bacterial alarmone ZMP through long-distance association of two RNA subdomains   pp679 - 685 Christopher P Jones and Adrian R Ferré-D'Amaré doi:10.1038/nsmb.3073 The cocrystal structure of bacterial alarmone ZMP with its cognate riboswitch reveals how the two subdomains of the latter mediate ligand recognition. Supporting biochemical analyses show that ligand binding affinity and transcription antitermination are modulated by the interdomain linker length. Probing Gαi1 protein activation at single-amino acid resolution   pp686 - 694 Dawei Sun, Tilman Flock, Xavier Deupi, Shoji Maeda, Milos Matkovic, Sandro Mendieta, Daniel Mayer, Roger J P Dawson, Gebhard F X Schertler, M Madan Babu & Dmitry B Veprintsev doi:10.1038/nsmb.3070 Extensive mutant cycle analysis provides a map of the residues that contribute to stability and activation-associated conformational dynamics of the Gαi1 protein in nucleotide-bound states and in complex with the G protein-coupled receptor rhodopsin. Structure of Rab11-FIP3-Rabin8 reveals simultaneous binding of FIP3 and Rabin8 effectors to Rab11   pp695 - 702 Melanie Vetter, Ralf Stehle, Claire Basquin and Esben Lorentzen doi:10.1038/nsmb.3065 Dual effector binding to the small GTPase Rab11 suggests that membrane-targeting complexes involved in vesicular transport might assemble through multiple weak interactions to create high-avidity assemblies. Structure and mechanism of activity-based inhibition of the EGF receptor by Mig6   pp703 - 711 Eunyoung Park, Nayoung Kim, Scott B Ficarro, Yi Zhang, Byung Il Lee, Ahye Cho, Kihong Kim, Angela K J Park, Woong-Yang Park, Bradley Murray, Matthew Meyerson, Rameen Beroukhim, Jarrod A Marto, Jeonghee Cho & Michael J Eck doi:10.1038/nsmb.3074 Mig6 phosphorylation at two consecutive tyrosines induces rearrangements that lead to Mig6 sticking to and inhibiting the same EGFR that catalyzed its phosphorylation. This mechanism may serve as a basis for inhibition of oncogenic EGFR variants. Ubp6 deubiquitinase controls conformational dynamics and substrate degradation of the 26S proteasome   pp712 - 719 Charlene Bashore, Corey M Dambacher, Ellen A Goodall, Mary E Matyskiela, Gabriel C Lander & Andreas Martin doi:10.1038/nsmb.3075 Electron microscopy and biochemistry analyses reveal that the deubiquitinase Ubp6, in its ubiquitin-bound form, inhibits substrate deubiquitination by Rpn11, stabilizes the proteasome in a substrate-engaged conformation and interferes with the engagement of a subsequent substrate. See also: News and Views by Yao Structure and mechanism of the Rubisco-assembly chaperone Raf1   pp720 - 728 Thomas Hauser, Javaid Y Bhat, Goran Miličić, Petra Wendler, F Ulrich Hartl, Andreas Bracher & Manajit Hayer-Hartl doi:10.1038/nsmb.3062 Biochemical and structural analyses show that Rubisco accumulation factor 1 (Raf1) stabilizes RbcL dimers, which then assemble into octamers. Raf1 is then displaced by RbcS, thus yielding the Rubisco holoenzyme. Crystal structures of the PsbS protein essential for photoprotection in plants   pp729 - 735 Minrui Fan, Mei Li, Zhenfeng Liu, Peng Cao, Xiaowei Pan,Hongmei Zhang, Xuelin Zhao, Jiping Zhang & Wenrui Chang doi:10.1038/nsmb.3068 PsbS is a transmembrane photosystem II protein essential for photoprotection in plants. Crystal structures show that PsbS is not a canonical pigment-binding protein and provide insights into its pH-dependent activation mechanism. See also: News and Views by Croce Recruitment and activation of the ATM kinase in the absence of DNA-damage sensors   pp736 - 743 Andrea J Hartlerode, Mary J Morgan, Yipin Wu, Jeffrey Buis and David O Ferguson doi:10.1038/nsmb.3072 The ATM kinase is shown to be recruited to sites of DNA damage, where it phosphorylates H2AX and triggers the G2-M checkpoint, in the absence of both MRN and Ku70-Ku80. The active site of O-GlcNAc transferase imposes constraints on substrate sequence   pp744 - 750 Shalini Pathak, Jana Alonso, Marianne Schimpl, Karim Rafie, David E Blair,Vladimir S Borodkin, Alexander W Schüttelkopf, Osama Albarbarawi & Daan M F van Aalten doi:10.1038/nsmb.3063 O-GlcNAcylation is a post-translational modification catalyzed by O-GlcNAc transferase. Here, a high-throughput activity assay combined with mass spectrometric and crystallographic analyses sheds light on the substrate recognition and specificity of O-GlcNAc transferase. Top Advertisement Nature Plants: Call for Papers Nature Plants launched in January and covers all aspects of plants be it their evolution, genetics, development or metabolism, their interactions with the environment, or their societal significance. 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