Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by {alpha}-amanitin [Protein Structure and Folding]

March 17th, 2018 by Xiangyang Liu, Lucas Farnung, Christoph Wigge, Patrick Cramer

RNA polymerase II (Pol II) is the central enzyme that transcribes eukaryotic protein-coding genes to produce mRNA. The mushroom toxin α-amanitin binds Pol II and inhibits transcription at the step of RNA chain elongation. Pol II from yeast binds α-amanitin with micromolar affinity, whereas metazoan Pol II enzymes exhibit nanomolar affinities. Here, we present the high-resolution cryo-EM structure of α-amanitin bound to and inhibited by its natural target, the mammalian Pol II elongation complex. The structure revealed that the toxin is located in a pocket previously identified in yeast Pol II, but forms additional contacts with metazoan-specific residues, which explain why its affinity to mammalian Pol II is ~3000 times higher than for yeast Pol II. Our work provides the structural basis for the inhibition of mammalian Pol II by the natural toxin α-amanitin and highlights that cryo-EM is well suited to studying interactions of a small molecule with its macromolecular target.

The major facilitator transporter Str3 is required for low-affinity heme acquisition in Schizosaccharomyces pombe [Microbiology]

March 16th, 2018 by Vincent Normant, Thierry Mourer, Simon Labbe

In the fission yeast Schizosaccharomyces pombe, acquisition of exogenous heme is largely mediated by the cell membrane-associated Shu1. Here, we report that Str3, a member of the major facilitator superfamily of transporters promotes cellular heme import. Using a strain that cannot synthesize heme de novo (hem1Δ) and lacks Shu1, we found that the heme-dependent growth deficit of this strain is rescued by hemin supplementation in the presence of Str3. Microscopic analyses of a hem1Δ shu1Δ str3Δ mutant strain in the presence of the heme analog zinc mesoporphyrin IX (ZnMP) revealed that ZnMP fails to accumulate within the mutant cells. In contrast, Str3-expressing hem1Δ shu1Δ cells could take up ZnMP at a 10-μM concentration. The yeast Saccharomyces cerevisiae cannot efficiently transport exogenously supplied hemin. However, heterologous expression of Str3 from S. pombe in S. cerevisiae resulted in ZnMP accumulation within S. cerevisiae cells. Moreover, hemin-agarose pulldown assays revealed that Str3 binds hemin. In contrast, a Str3 mutant in which Tyr and Ser residues of two putative heme-binding motifs (530Y-X3-Y534 and 552S-X4-Y557) had been replaced with alanines exhibited a loss of affinity for hemin. Furthermore, this Str3 mutant failed to rescue the heme-dependent growth deficit of a hem1Δ shu1Δ str3Δ strain. Further analysis by absorbance spectroscopy disclosed that a predicted extracellular loop region in Str3 containing the two putative heme-binding motifs interacts with hemin, with a KD of 6.6 μM. Taken together, these results indicate that Str3 is a second cell-surface membrane protein for acquisition of exogenous heme in S. pombe.

Relationship of Sequence and Phase Separation in Protein Low-Complexity Regions

March 16th, 2018 by Erik W. Martin and Tanja Mittag

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Biochemistry
DOI: 10.1021/acs.biochem.8b00008

Characterization of 1,2-Propanediol Dehydratases Reveals Distinct Mechanisms for B12-Dependent and Glycyl Radical Enzymes

March 16th, 2018 by Benjamin J. Levin and Emily P. Balskus

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Biochemistry
DOI: 10.1021/acs.biochem.8b00164

Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis

March 12th, 2018 by Sean A. Newmister

Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis

Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis, Published online: 12 March 2018; doi:10.1038/s41589-018-0003-x

The structure of a Stig cyclase, HpiC1, reveals how it catalyzes Cope rearrangement and 6-exo-trig cyclization, including how it controls the position of electrophilic aromatic substation that distinguishes hapalindole from fischerindole alkaloids.
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Photophysical Tuning of N-Oxide-Based Probes Enables Ratiometric Photoacoustic Imaging of Tumor Hypoxia

March 9th, 2018 by Hailey J. Knox, Tae Wook Kim, Zhouyang Zhu and Jefferson Chan

TOC Graphic

ACS Chemical Biology
DOI: 10.1021/acschembio.8b00099
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Publisher Correction: Oxidative demethylation of algal carbohydrates by cytochrome P450 monooxygenases

March 8th, 2018 by Lukas Reisky

Publisher Correction: Oxidative demethylation of algal carbohydrates by cytochrome P450 monooxygenases

Publisher Correction: Oxidative demethylation of algal carbohydrates by cytochrome P450 monooxygenases, Published online: 08 March 2018; doi:10.1038/s41589-018-0020-9

Publisher Correction: Oxidative demethylation of algal carbohydrates by cytochrome P450 monooxygenases
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Publisher Correction: A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

March 8th, 2018 by Kiryl D. Piatkevich

Publisher Correction: A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters

Publisher Correction: A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters, Published online: 08 March 2018; doi:10.1038/s41589-018-0023-6

Publisher Correction: A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters
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Publisher Correction: Resistance to nonribosomal peptide antibiotics mediated by <span class=”small-caps”>d</span>-stereospecific peptidases

March 7th, 2018 by Yong-Xin Li

Publisher Correction: Resistance to nonribosomal peptide antibiotics mediated by d-stereospecific peptidases

Publisher Correction: Resistance to nonribosomal peptide antibiotics mediated by <span class="small-caps">d</span>-stereospecific peptidases, Published online: 07 March 2018; doi:10.1038/s41589-018-0022-7

Publisher Correction: Resistance to nonribosomal peptide antibiotics mediated by d-stereospecific peptidases
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Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins

March 5th, 2018 by Pierre Goloubinoff

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins

Chaperones convert the energy from ATP into the nonequilibrium stabilization of native proteins, Published online: 05 March 2018; doi:10.1038/s41589-018-0013-8

A nonequilibrium thermodynamic model can explain how molecular chaperones such as GroEL can use the energy from ATP hydrolysis to maintain substrate proteins in an active state, even under conditions that favor the substrate’s inactive unfolded state.
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