Featured
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| Open AccessThe evolutionary advantage of an aromatic clamp in plant family 3 glycoside exo-hydrolases
Barley β-d-glucan glucohydrolase is a glycoside hydrolase family 3 (GH3) enzyme critical for growth and development. Here the authors carryout mutagenesis, structural analyses and multi-scale molecular dynamics to examine the binding and conformational behaviour of several β-d-glucosides during the substrate-product assisted catalysis that operates in GH3 hydrolases.
- Sukanya Luang
- , Xavier Fernández-Luengo
- & Maria Hrmova
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Article
| Open AccessMechanistic understanding of human SLFN11
Schlafen 11 serves as an antiviral restriction factor and a predictive biomarker in cancer. Here, the authors use cryoelectron microscopy and biochemical assays to understand tRNA endoribonuclease and DNA binding functions of human Schlafen 11.
- Felix J. Metzner
- , Simon J. Wenzl
- & Katja Lammens
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| Open AccessBiochemical and structural insights of multifunctional flavin-dependent monooxygenase FlsO1-catalyzed unexpected xanthone formation
The biosynthesis of xanthones has not been well documented. Here, the authors report that monooxygenase FlsO1 catalyzes three successive oxidations – hydroxylation, epoxidation and Baeyer–Villiger oxidation—to form the xanthone scaffold in actinomycetes.
- Chunfang Yang
- , Liping Zhang
- & Changsheng Zhang
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Article
| Open AccessStructure of the membrane-bound formate hydrogenlyase complex from Escherichia coli
New cryo-EM structures of the formate hydrogenlyase complex from the model bacterium E. coli clarify how electrons and protons move through the complex and are combined to make H2 gas. The complex shows important similarities and differences to related bioenergetic complexes across the tree of life.
- Ralf Steinhilper
- , Gabriele Höff
- & Bonnie J. Murphy
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Article
| Open AccessDepletable peroxidase-like activity of Fe3O4 nanozymes accompanied with separate migration of electrons and iron ions
The mechanism of peroxidase-like Fe3O4 nanozymes remains elusive. Here, the authors show the electron transfer mechanism of Fe(II) ions to regenerate surface Fe(II) and the related phase transformation and depletion of activity.
- Haijiao Dong
- , Wei Du
- & Yu Zhang
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Article
| Open AccessElucidation of divergent desaturation pathways in the formation of vinyl isonitrile and isocyanoacrylate
While canonical oxygen-rebound pathway has been utilized by several Fe/2OG enzymes, insights into the desaturation process remain to be elucidated. Here, the authors suggest that a carbocation might be deployed to enable chemically divergent desaturations through decarboxylation and deprotonation.
- Wantae Kim
- , Tzu-Yu Chen
- & Wei-chen Chang
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Article
| Open AccessAllosteric inhibition of HTRA1 activity by a conformational lock mechanism to treat age-related macular degeneration
The protease HTRA1 is a genetic risk factor for geographic atrophy. Here, Gerhardy et al. describe its inhibition by a clinical Fab, whose binding locks it in an inactive state. The mechanism identifies an essential function of LoopA with this protease family.
- Stefan Gerhardy
- , Mark Ultsch
- & Daniel Kirchhofer
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| Open AccessX-ray crystallographic characterization of the SARS-CoV-2 main protease polyprotein cleavage sites essential for viral processing and maturation
The SARS-CoV-2 protease Mpro is essential for viral replication. Here, the authors have determined the structures of Mpro in complex with 10 of the 11 viral cleavage sequences including a covalent acyl-enzyme intermediate, providing mechanistic and structural insights for antiviral development.
- Jaeyong Lee
- , Calem Kenward
- & Mark Paetzel
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Article
| Open AccessStructural bases for aspartate recognition and polymerization efficiency of cyanobacterial cyanophycin synthetase
CphA1 catalyzes the synthesis of cyanophycin polypeptide consisting of equimolar amounts of aspartate and arginine as a fixed nitrogen reservoir in cyanobacteria. Here, the authors solve the cryo-EM structures of CphA1, revealing the aspartate binding mode and protein dynamics required for cyanophycin elongation.
- Takuya Miyakawa
- , Jian Yang
- & Masaru Tanokura
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Article
| Open AccessDirected evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform
Engineering enzymes to utilize the noncanonical redox cofactors such as nicotinamide mononucleotide (NMN + ) is challenging. Here, the authors report a growth-based selection platform for NMN + -reducing enzyme engineering and show its application in developing a phosphite dehydrogenase with improved catalytic efficiency.
- Linyue Zhang
- , Edward King
- & Han Li
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Article
| Open AccessCrystal structures reveal catalytic and regulatory mechanisms of the dual-specificity ubiquitin/FAT10 E1 enzyme Uba6
Uba6 is an E1 enzyme that regulates numerous cellular processes by activating ubiquitin and FAT10 pathways. Here, the authors present crystal structures that illuminate Uba6 catalytic mechanisms and reveal inositol hexakisphosphate as a cofactor that modulates Uba6 activity.
- Lingmin Yuan
- , Fei Gao
- & Shaun K. Olsen
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Article
| Open AccessHydrogen-bonded organic framework biomimetic entrapment allowing non-native biocatalytic activity in enzyme
Heme units are immobilised in diverse heme enzymes for oxidation, and have been immobilised also in hydrogen-bonded organic frameworks. Here, the authors show the use of hydrogen-bonded organic framework to modulate the enzyme’s conformation and show different biofunction from the original.
- Guosheng Chen
- , Linjing Tong
- & Gangfeng Ouyang
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Article
| Open AccessStructures of UBA6 explain its dual specificity for ubiquitin and FAT10
UBA6 is an E1 enzyme that can activate both ubiquitin and FAT10. Here, the authors employ X-ray crystallography and biochemical techniques to explain this dual specificity, and identify UBA6 variants that are selectively impaired in the activation of either ubiquitin or FAT10.
- Ngoc Truongvan
- , Shurong Li
- & Hermann Schindelin
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Article
| Open AccessBiocatalytic routes to stereo-divergent iridoids
Iridoid compounds are an important class of natural products. Here, the authors report on the discovery and engineering of nepetalactol-related short chain reductases and their application for the biosynthesis of nepetalactol or nepetalactone stereoisomers, as a versatile system for the production of the iridoid natural product scaffold.
- Néstor J. Hernández Lozada
- , Benke Hong
- & Sarah E. O’Connor
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Article
| Open AccessStructural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β
The authors revealed novel roles of catalytic residues and divalent metal ions for hsTOP3B, the human RNA topoisomerase, and demonstrated the structural elements that kinetically modulate the DNA and RNA topoisomerase activities of TOP3B.
- Xi Yang
- , Sourav Saha
- & Yves Pommier
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Article
| Open AccessMet1-specific motifs conserved in OTUB subfamily of green plants enable rice OTUB1 to hydrolyse Met1 ubiquitin chains
Deubiquitinases (DUBs) targeting Met1-linked ubiquitin chains have important functions in mammals but are barely studied in plants. Here, the authors identify rice OTUB1 as a Met1-targeting DUB, characterize the structural determinants of this activity, and show that these features are conserved in green plants.
- Lining Lu
- , Xiaoguo Zhai
- & Feng Wang
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Article
| Open AccessMultistep orthophosphate release tunes actomyosin energy transduction
Release of the ATP hydrolysis product orthophosphate (Pi) from the myosin active site is central in force generation but is poorly understood. Here, Moretto et al. present evidence for multistep Pi-release reconciling apparently contradictory results.
- Luisa Moretto
- , Marko Ušaj
- & Alf Månsson
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Article
| Open AccessRegulatory mechanisms of lipopolysaccharide synthesis in Escherichia coli
Synthesis of lipopolysaccharides, essential components for most gram-negative bacteria, is under tight control. Here, authors use in vitro reconstitution and structural approaches to elucidate some of these regulatory mechanisms involving essential membrane proteins LapB and YejM.
- Sheng Shu
- & Wei Mi
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Article
| Open AccessAvmM catalyses macrocyclization through dehydration/Michael-type addition in alchivemycin A biosynthesis
Macrocyclization is an important process in bioactive natural product synthesis. Here, the authors report on the study of a macrocyclic ring constructing enzyme in the biosynthesis of alchivemycin A and using gene deletion, biochemical assays and isotope labelling show the enzyme catalyses tandem dehydration and Michael-type addition.
- Hong Jie Zhu
- , Bo Zhang
- & Hui Ming Ge
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Article
| Open AccessMolecular and in vivo studies of a glutamate-class prolyl-endopeptidase for coeliac disease therapy
Celiac disease is characterized by intolerance to gluten, a cereal protein. Here, the authors show that neprosin, a glutamate peptidase from the pitcher plant, efficiently cleaves gluten components under physiological conditions in vitro and in the gut of mice.
- Laura del Amo-Maestro
- , Soraia R. Mendes
- & F. Xavier Gomis-Rüth
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Article
| Open AccessMolecular mechanism of toxin neutralization in the HipBST toxin-antitoxin system of Legionella pneumophila
Here, the authors demonstrate that the Legionella pneumophila T4SS effector protein Lpg2370 is a Ser/Thr kinase and a toxin of a tripartite HipBST toxin-antitoxin (TA) system. Structural data and biochemical analysis provide detailed insights into the toxin neutralization mechanism in the HipBST TA.
- Xiangkai Zhen
- , Yongyu Wu
- & Songying Ouyang
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Article
| Open AccessStructural and mechanistic insights into the cleavage of clustered O-glycan patches-containing glycoproteins by mucinases of the human gut
AM0627 is a bis-O-glycan mucinase that might work in the final steps of mucus degradation, thereby providing a carbon and nitrogen source for Akkermansia muciniphila. Here, the authors provide molecular insights into AM0627 function from X-ray crystallography and computer simulations.
- Víctor Taleb
- , Qinghua Liao
- & Ramon Hurtado-Guerrero
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Article
| Open AccessCryo-EM structures of Na+-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae
The Na+-pumping NADH-ubiquinone oxidoreductase (Na+-NQR) is a unique respiratory enzyme found in many pathogenic bacteria. Here, the authors present high-resolution cryo-EM structures of Na+-NQR from V. cholerae with or without a bound inhibitor.
- Jun-ichi Kishikawa
- , Moe Ishikawa
- & Hideto Miyoshi
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Article
| Open AccessMechanism of threonine ADP-ribosylation of F-actin by a Tc toxin
Entomopathogenic bacteria used for pest control secrete potent Tc toxins. Here, the authors combine biochemistry, solution and solid-state NMR spectroscopy and cryo-EM to show in atomic detail how the toxin disrupts the host cell cytoskeleton and kills the target cell.
- Alexander Belyy
- , Florian Lindemann
- & Stefan Raunser
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Article
| Open AccessKinesin-8-specific loop-2 controls the dual activities of the motor domain according to tubulin protofilament shape
Kinesin-8s are dual-activity motor proteins that can move processively on microtubules and depolymerize microtubule plus-ends. This study shows how kinesin-8s alternate between a promotility and a pro-microtubule-depolymerization state via their tubulin shape-sensing loop-2 region.
- Byron Hunter
- , Matthieu P. M. H. Benoit
- & John S. Allingham
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Article
| Open AccessSingle-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2
Single-molecule FRET measurements provide detailed insights into the conformational states and dynamics of human Argonaute 2 that are required for its function at the core of the eukaryotic RNA silencing pathway.
- Sarah Willkomm
- , Leonhard Jakob
- & Dina Grohmann
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Article
| Open AccessMapping the conformational energy landscape of Abl kinase using ClyA nanopore tweezers
Quantitative characterization of kinase conformational dynamics remains challenging. Here, the authors show that protein nanopore tweezers allow analyzing the conformational energy landscape and ligand binding of the Abl kinase domain.
- Fanjun Li
- , Monifa A. Fahie
- & Min Chen
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Article
| Open AccessMechanism of glycogen synthase inactivation and interaction with glycogenin
Glycogen is a major energy reserve in eukaryotes and is synthesised in part by glycogenin (GN) and glycogen synthase (GS). Here, authors describe the structural basis of GS regulation, specifically the mechanism of inactivation by phosphorylation.
- Laura Marr
- , Dipsikha Biswas
- & Elton Zeqiraj
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Article
| Open AccessWatching right and wrong nucleotide insertion captures hidden polymerase fidelity checkpoints
DNA polymerase (pol) λ performs DNA synthesis in base excision and double strand break repair. How pol λ accomplishes nucleotide insertion that can lead to mutagenesis and genomic instability was unclear. Here the authors employ time-lapse crystallography to reveal hidden polymerase checkpoints that enable right and wrong natural nucleotide insertion by pol λ.
- Joonas A. Jamsen
- , David D. Shock
- & Samuel H. Wilson
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Article
| Open AccessA Catharanthus roseus Fe(II)/α-ketoglutarate-dependent dioxygenase catalyzes a redox-neutral reaction responsible for vindolinine biosynthesis
Catharanthus roseus is the source for anticancer drug vinblastine and other medicinal monoterpenoid indole alkaloids. Here the authors characterize an Fe/2OG dioxygenase, vindolinine synthase, which catalyzes an unusual redox-neutral reaction leading to alkaloid diversity.
- Jasmine Ga May Eng
- , Mohammadamin Shahsavarani
- & Yang Qu
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Article
| Open AccessThe structure of EXTL3 helps to explain the different roles of bi-domain exostosins in heparan sulfate synthesis
Heparan sulphate (HS)—a common cell surface decoration—is a carbohydrate of alternating sugars assembled by bi-domain enzymes such as EXTL3. Here, authors present the structure of EXTL3, explain EXTL3 lost activity, and propose that HS extension is distributive.
- L. F. L. Wilson
- , T. Dendooven
- & P. Dupree
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Article
| Open AccessStructural basis for MTA1c-mediated DNA N6-adenine methylation
DNA N6-adenine methylation (6 mA) plays a crucial role in epigenetic regulation in eukaryotes. Here, the authors determined nine crystal structures of the ciliates 6 mA methyltransferase complexes, providing the molecular basis for understanding the functions of 6 mA.
- Jiyun Chen
- , Rong Hu
- & Liang Liu
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Article
| Open AccessStructural basis for broad anti-phage immunity by DISARM
DISARM (Defense Island System Associated with Restriction Modification) systems can provide bacteria with protection against a wide range of phage. Here, Bravo et al. determine cryo-EM structures of the core DISARM complex that shed light onto phage DNA recognition and activation of this widespread defense system.
- Jack P. K. Bravo
- , Cristian Aparicio-Maldonado
- & David W. Taylor
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Article
| Open AccessInsights into methionine S-methylation in diverse organisms
S-methyl methionine (SMM) is a key molecule in production of dimethylsulfoniopropionate (DMSP), an important marine anti-stress compound, with roles in global nutrient cycling. Here, the authors determine the mechanism of SMM synthesis and uncover unexpected roles for SMM in archaea, CPR bacteria and animals.
- Ming Peng
- , Chun-Yang Li
- & Yu-Zhong Zhang
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Article
| Open AccessCryo-EM structures define ubiquinone-10 binding to mitochondrial complex I and conformational transitions accompanying Q-site occupancy
Using cryo-EM, Chung et al. investigate conformational states of mammalian respiratory complex I to reveal an ubiquinone-10 molecule occupying the full length of the Q-binding channel. Molecular dynamics simulations suggest how the charge states of key residues influence the substrate binding pose.
- Injae Chung
- , John J. Wright
- & Judy Hirst
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Article
| Open AccessActive conformation of the p97-p47 unfoldase complex
The p97 unfoldase is an essential and abundant enzyme that segregates its substrates from macromolecular complexes and organelle membranes. Here, authors determined the structure of human p97 in the act of unfolding an authentic substrate.
- Yang Xu
- , Han Han
- & Peter S. Shen
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Article
| Open AccessDiscovery and characterization of a terpene biosynthetic pathway featuring a norbornene-forming Diels-Alderase
Pericyclase enzymes are an expanding family of enzymes. Here, the authors identify the norbornene synthase SdnG, a pericyclase for the intramolecular Diels-Alder reaction between a cyclopentadiene and an olefinic dienophile to form the sordaricin norbornene structure, and reconstitute the sordaricin biosynthesis.
- Zuodong Sun
- , Cooper S. Jamieson
- & Yi Tang
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Article
| Open AccessStatin therapy inhibits fatty acid synthase via dynamic protein modifications
Statin therapy is associated with numerous cellular effects. Here, the authors show that statin treatment increases post-translational modifications on fatty acid synthase in the active site, revealing communication between the cholesterol and lipid biosynthetic pathways.
- Alec G. Trub
- , Gregory R. Wagner
- & Matthew D. Hirschey
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Article
| Open AccessStructural basis for the synthesis of the core 1 structure by C1GalT1
The glycosyltransferase C1GalT1 directs a key step in protein O-glycosylation important for the expression of the cancer-associated Tn and T antigens. Here, the authors provide molecular insights into the function of C1GalT1 by solving the crystal structure of the Drosophila enzyme-substrate complex.
- Andrés Manuel González-Ramírez
- , Ana Sofia Grosso
- & Ramon Hurtado-Guerrero
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Article
| Open AccessA structural exposé of noncanonical molecular reactivity within the protein tyrosine phosphatase WPD loop
Inositol pyrophosphates (PP-IPs) regulate immunity and phosphate homeostasis. Here, the authors’ structural dissection of an Arabidopsis thaliana PP-IP phosphatase reveals that substrates drive their own hydrolysis and identifies a highly elusive metaphosphate-like reaction intermediate.
- Huanchen Wang
- , Lalith Perera
- & Stephen B. Shears
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Article
| Open AccessSecondary structure RNA elements control the cleavage activity of DICER
MicroRNA precursors are cleaved by DICER to generate mature microRNAs in the cytoplasm. Here the authors employ high-throughput analysis of DICER cleavage activity and identify RNA secondary elements in precursor miRNAs and shRNAs, including a single nucleotide bulge, which govern its cleavage efficiency and accuracy.
- Trung Duc Nguyen
- , Tam Anh Trinh
- & Tuan Anh Nguyen
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Article
| Open AccessStructural basis for the mechanisms of human presequence protease conformational switch and substrate recognition
Presequence protease (PreP) is essential to mitochondrial proteostasis. This study leverages advanced vitrification techniques to solve cryoEM structures of apo- and substrate-bound PreP and integrates these data with other analysis to reveal key stages and mechanistic insights of the PreP catalytic cycle.
- Wenguang G. Liang
- , Juwina Wijaya
- & Wei-Jen Tang
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Article
| Open AccessAuxiliary ATP binding sites support DNA unwinding by RecBCD
RecBCD is a remarkably fast DNA helicase. Using a battery of biophysical methods, Zananiri et. al reveal additional, non-catalytic ATP binding sites that increase the ATP flux to the catalytic sites that allows fast unwinding when ATP is scarce.
- Rani Zananiri
- , Sivasubramanyan Mangapuram Venkata
- & Arnon Henn
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Article
| Open AccessNeural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations
Here, the authors apply a neural relational inference model to infer dynamic networks of interacting residues in protein molecular dynamics simulations. The model can predict allosteric communication pathways and relative free energy changes upon mutations.
- Jingxuan Zhu
- , Juexin Wang
- & Dong Xu
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Article
| Open AccessExpanding biochemical knowledge and illuminating metabolic dark matter with ATLASx
“Mapping the dark matter of metabolism remains an open challenge that can be addressed globally and systematically by existing computational solutions. Here the authors present ATLASx, a repository of known and predicted enzymatic reaction, connecting millions of compounds to help synthetic biologists and metabolic engineers to design and explore metabolic pathways.”
- Homa MohammadiPeyhani
- , Jasmin Hafner
- & Vassily Hatzimanikatis
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Article
| Open AccessTranscription factors modulate RNA polymerase conformational equilibrium
Pausing of RNA polymerase (RNAP) and transcription is regulated by the NusA and NusG transcription factors in bacteria. Here the authors provide structural evidence for how they interact with RNAP to carry out their pausing roles and also reveal functions for NusA and NusG in transcription termination.
- Chengjin Zhu
- , Xieyang Guo
- & Albert Weixlbaumer
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Article
| Open AccessMechanism and biomass association of glucuronoyl esterase: an α/β hydrolase with potential in biomass conversion
Zong and coworkers combine computational and experimental methods to decipher in detail the mechanism of action of glucuronoyl esterases, enzymes with significant biotechnological potential for decoupling lignin from polysaccharides in biomass.
- Zhiyou Zong
- , Scott Mazurkewich
- & Leila Lo Leggio
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Article
| Open AccessStructural Insight into the MCM double hexamer activation by Dbf4-Cdc7 kinase
The Dbf4-dependent kinase Cdc7 (DDK) is essential for eukaryotic DNA replication. Here, the authors present a series of cryo-EM structures elucidating the versatility of this kinase in exerting an ordered phosphorylation of its essential target to promote replication initiation.
- Jiaxuan Cheng
- , Ningning Li
- & Yuanliang Zhai
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Article
| Open AccessA kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity
Cas9 off-target sites can be predicted by many bioinformatics tools. Here the authors present low complexity mechanistic model that characterizes SpCas9 kinetics in free-energy terms, allowing quantitative prediction of off-target activity in bulk-biochemistry, single molecule, and whole-genome profiling experiments.
- Behrouz Eslami-Mossallam
- , Misha Klein
- & Martin Depken