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| Open AccessA gene cluster in Ginkgo biloba encodes unique multifunctional cytochrome P450s that initiate ginkgolide biosynthesis
Although ginkgo terpenoids have been studied extensively for their pharmaceutical properties, knowledge on their biosynthesis remains limited. Here, the authors identify five multifunctional cytochrome P450s that catalyze the generation of the tert-butyl group and one of the lactone rings towards the biosynthesis of ginkgolides.
- Victor Forman
- , Dan Luo
- & Irini Pateraki
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Article
| Open AccessStructural and mechanistic basis for recognition of alternative tRNA precursor substrates by bacterial ribonuclease P
Ribonuclease P efficiently processes all tRNA precursors despite sequence variation at the site of cleavage. Here, authors use high-throughput enzymology and cryoEM to reveal conformational changes that drive recognition by bacterial RNase P.
- Jiaqiang Zhu
- , Wei Huang
- & Michael E. Harris
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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 AccessChemical zymogens for the protein cysteinome
Reversible on/off switches for enzyme activity are foundational in nature but are challenging to design using tools of synthetic chemistry. Here the authors design chemical zymogens amenable for activation via biomolecular interactions.
- Mireia Casanovas Montasell
- , Pere Monge
- & Alexander N. Zelikin
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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 AccessResistance to the isocitrate dehydrogenase 1 mutant inhibitor ivosidenib can be overcome by alternative dimer-interface binding inhibitors
The development of IDH variant inhibitors is a breakthrough as it is the first time metabolism has been successfully targeted by small molecule drugs in cancer. Here the authors report studies on resistance to the pioneer drug ivosidenib leading to identification of inhibitors retaining activity.
- Raphael Reinbold
- , Ingvild C. Hvinden
- & Christopher J. Schofield
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Article
| Open AccessSingle-atom nanozymes catalytically surpassing naturally occurring enzymes as sustained stitching for brain trauma
The catalytic activity of regenerable nanozymes is currently the bottle neck for their wider employment. Here, the authors report on single-atom nanozymes of RhN4, VN4, and Fe-Cu-N6 with higher catalytic activities than natural enzymes, and demonstrate the Rh/VN4 recyclability and scalp healing properties in bioactive sutures.
- Shaofang Zhang
- , Yonghui Li
- & Xiao-Dong Zhang
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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 AccessAdenosine triphosphate-activated prodrug system for on-demand bacterial inactivation and wound disinfection
Prodrugs are increasingly promising in tackling bacterial resistance and efficacy of treatment. Here, the authors encapsulated horseradish peroxidase and zeolitic imidazolate framework-8 loaded with indole-3-acetic acid in polyacrylamide hydrogel microspheres for ATP-activated wound disinfection.
- Yuhao Weng
- , Huihong Chen
- & Hongliang Tan
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Article
| Open AccessNative metabolomics identifies the rivulariapeptolide family of protease inhibitors
Bioactivity-guided isolation of specialized metabolites is an iterative process. Here, the authors demonstrate a native metabolomics approach that allows for fast screening of complex metabolite extracts against a protein of interest and simultaneous structure annotation.
- Raphael Reher
- , Allegra T. Aron
- & Daniel Petras
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Article
| Open AccessLigand-specific conformational change drives interdomain allostery in Pin1
Born et al. describe interdomain allostery in the two domain peptidyl-prolyl isomerase Pin1 upon binding of two ligands. These ligands couple population shifts of extended and compact states to changes in the catalytic site of Pin1.
- Alexandra Born
- , Janne Soetbeer
- & Beat Vögeli
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Article
| Open AccessGolgi stress induces SIRT2 to counteract Shigella infection via defatty-acylation
Here the authors revealed a role for the protein deacetylase SIRT2 in Golgi stress, particularly induced by bacterial infection. Shigella secrete effector proteins such as IcsB, which transfers fatty acyl groups to modify host proteins to evade host immune surveillance. The upregulated SIRT2 counteracts this function by removing the fatty acyl groups and enhancing the killing of Shigella.
- Miao Wang
- , Yugang Zhang
- & Hening Lin
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Article
| Open AccessRegulated degradation of HMG CoA reductase requires conformational changes in sterol-sensing domain
HMG-CoA reductase (HMGCR) is regulated by UBIAD1 and Insigs and initializes cholesterol synthesis. Here authors show that the sterol sensing domain of HMGCR undergoes conformational changes to regulate its degradation via binding its protein modulators.
- Hongwen Chen
- , Xiaofeng Qi
- & Xiaochun Li
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Article
| Open AccessA cryptic third active site in cyanophycin synthetase creates primers for polymerization
Cyanophycin synthetase CphA1 polymerizes Asp and Arg into the nitrogen reserve polymer cyanophycin using two active sites. Sharon et al. show CphA1 has a cryptic 3rd active site that cleaves cyanophycin into primers for self-sufficient biosynthesis.
- Itai Sharon
- , Sharon Pinus
- & T. Martin Schmeing
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Article
| Open AccessSpatial regulation of AMPK signaling revealed by a sensitive kinase activity reporter
AMP activated protein kinase (AMPK) is a master regulator of cellular metabolism, but how AMPK activity is spatiotemporally regulated remains unclear. Here, Schmitt et al develop a sensitive biosensor for AMPK, which they use to uncover mechanisms for AMPK activity in the lysosome and nucleus.
- Danielle L. Schmitt
- , Stephanie D. Curtis
- & Jin Zhang
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Article
| Open AccessStructures of LIG1 that engage with mutagenic mismatches inserted by polβ in base excision repair
Ligase I seals two ends of DNA during DNA repair and replication. Here — solving structures of Ligase I with imperfect DNA harboring mismatches incorporated by DNA polymerase — the authors reveal how the repair proteins maintain fidelity at final ligation step.
- Qun Tang
- , Mitchell Gulkis
- & Melike Çağlayan
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Article
| Open AccessEmergent properties as by-products of prebiotic evolution of aminoacylation ribozymes
Complex biochemical systems exhibit traits that appear to be highly adapted. Studies of catalytic RNA demonstrate that adaptive traits, such as increased specificity and error tolerance, could originate as evolutionary by-products.
- Evan Janzen
- , Yuning Shen
- & Irene A. Chen
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Article
| Open AccessEngineering substrate specificity of HAD phosphatases and multienzyme systems development for the thermodynamic-driven manufacturing sugars
Haloacid dehalogenase-like phosphatases are widespread across all domains of life and play a crucial role in the regulation of levels of sugar phosphate metabolites in cells. The authors report on the structure-guided engineering of phosphatases for dedicated substrate specificity for the conversion of sucrose and starch into fructose and mannose.
- Chaoyu Tian
- , Jiangang Yang
- & Yanhe Ma
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Article
| Open AccessComplete biosynthetic pathway to the antidiabetic drug acarbose
The market demand for acarbose, a drug used for treatment of patients affected by type-2 diabetes, has increased. In this article, the authors report the acarbose complete biosynthetic pathway, clarifying previously unknown steps and identifying a pseudoglycosyltransferase enzyme, AcbS, a homologue of AcbI that catalyzes the formation of a non-glycosidic C-N bond.
- Takeshi Tsunoda
- , Arash Samadi
- & Taifo Mahmud
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Article
| Open AccessStructural basis of resistance to herbicides that target acetohydroxyacid synthase
Acetohydroxyacid synthase (AHAS) is the target of more than 50 commercial herbicides, with many site-of-action resistance isolates identified in weeds. Here, the authors report the structural and kinetic characterizations to explain the effect AHAS mutations have on herbicide potency.
- Thierry Lonhienne
- , Yan Cheng
- & Luke W. Guddat
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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 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 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 AccessMechanism of nucleotide discrimination by the translesion synthesis polymerase Rev1
Rev1 is a specialized translesion synthesis DNA polymerase involved in the bypass DNA damage during DNA replication. Here, the authors determine the structural basis for preferential incorporation of dCTP by Rev1 during bypass of DNA damage.
- Tyler M. Weaver
- , Timothy H. Click
- & Bret D. Freudenthal
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Article
| Open AccessMolecular insights into biogenesis of glycosylphosphatidylinositol anchor proteins
GPI-T catalyzes the committed step in GPI anchor protein biogenesis. Here, Xu et al. report the cryo-EM structure of the human GPI-T, revealing critical elements within an elongated, shared active site which is topologically arranged for substrate specificity.
- Yidan Xu
- , Guowen Jia
- & Dianfan Li
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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 AccessRadical SAM-dependent ether crosslink in daropeptide biosynthesis
Darobactin is a ribosomally synthesized and post-translationally modified peptide featuring a unique scaffold and potent activity against Gram-negative bacteria. Here, the authors identify darobactin synthase DarE as responsible for the bicyclic scaffold formation and propose the name daropeptide for this growing class of enzymes.
- Sijia Guo
- , Shu Wang
- & Qi Zhang
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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 AccessCyclic 5-membered disulfides are not selective substrates of thioredoxin reductase, but are opened nonspecifically
Cyclic five-membered disulfides (1,2-dithiolanes) have been reported either as nonspecific redox motifs, or as highly specific cellular probes for thioredoxin reductase (TrxR). Here the authors show that 1,2-dithiolane probes are nonspecifically reduced by a range of thiol reductants and are not sensitive to TrxR modulation, thus they are unsuitable as cellular probes for TrxR.
- Jan G. Felber
- , Lena Poczka
- & Oliver Thorn-Seshold
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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 AccessGlobal profiling of regulatory elements in the histone benzoylation pathway
Lysine benzoylation (Kbz) is a recently discovered histone modification. Here, the authors characterize writers, erasers and readers of histone Kbz in S. cerevisiae and identify non-histone proteins bearing Kbz, laying foundations to dissect the roles of Kbz in diverse cellular processes.
- Duo Wang
- , Fuxiang Yan
- & Yong Chen
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Article
| Open AccessMachine learning discovery of missing links that mediate alternative branches to plant alkaloids
Producing plant secondary metabolites by microbes is limited by the known enzymatic reactions. Here, the authors apply machine learning to predict missing link enzymes of benzylisoquinoline alkaloid (BIA) biosynthesis in Papaver somniferum, and validate the specialized activities through heterologous production.
- Christopher J. Vavricka
- , Shunsuke Takahashi
- & Tomohisa Hasunuma
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Article
| Open AccessAtomically unveiling the structure-activity relationship of biomacromolecule-metal-organic frameworks symbiotic crystal
Biomolecule-metal-organic-frameworks allow for the creation of hybrid materials with desired biological and chemical function. Here, the authors refine the structure-function relationship by identifying the atomic-layer structure of the hybrids and show differences in structure upon different crystallisation pathways.
- Linjing Tong
- , Siming Huang
- & Gangfeng Ouyang
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Article
| Open AccessReconstituting the complete biosynthesis of D-lysergic acid in yeast
The ergot alkaloids are a class of natural products known for their pharmacologically privileged molecular structure that are used in the treatment of neurological ailments. Here the authors report on the production of the ergot (fungus)-derived therapeutic precursor, D-lysergic acid (DLA), in baker’s yeast.
- Garrett Wong
- , Li Rong Lim
- & Wen Shan Yew
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Article
| Open AccessThe toposiomerase IIIalpha-RMI1-RMI2 complex orients human Bloom’s syndrome helicase for efficient disruption of D-loops
Human Bloom’s syndrome (BLM) helicase has a role in DNA repair, and BLM deficiency in humans is associated with chromosomal abnormalities. Here the authors employ solution biophysical assays to show BLM maintains a balance for disruption and stabilization of oligonucleotide-based D-loops. Interaction with the Topoisomerase IIIalpha-RMI1-RMI2 complex orients the activity toward D-loop disruption.
- Gábor M. Harami
- , János Pálinkás
- & Mihály Kovács
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Article
| Open AccessA dual mechanism of action of AT-527 against SARS-CoV-2 polymerase
The drug AT-527 targets the SARS-CoV-2 replication machinery. Here the authors use Cryo-EM to show how AT-527 inhibits SARS-CoV-2 polymerase by acting as an immediate RNA chain terminator and stably binding in a NiRAN active-site pocket; impeding an essential nucleotide-transfer activity.
- Ashleigh Shannon
- , Véronique Fattorini
- & Bruno Canard
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Article
| Open AccessStructures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module
Nonribosomal peptide synthetases work with additional enzymes to synthesise secondary metabolites and therapeutics. Here, the authors explore bacillamide D synthesis and show the oxidase action is done while the intermediate is attached to the synthetase and replicate this with an oxidase bound synthetase for bioengineering applications.
- Camille Marie Fortinez
- , Kristjan Bloudoff
- & T. Martin Schmeing
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Article
| Open AccessThe RNA methyltransferase METTL8 installs m3C32 in mitochondrial tRNAsThr/Ser(UCN) to optimise tRNA structure and mitochondrial translation
RNA modifications are key regulators of RNA functions. Here, the authors identify METTL8 as the enzyme installing m3C32 in mitochondrial tRNAThr/Ser(UCN). Lack of these modifications affects tRNA structure and impairs mitochondrial translation.
- Nicole Kleiber
- , Nicolas Lemus-Diaz
- & Markus T. Bohnsack
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Article
| Open AccessTransglutaminase 3 crosslinks the secreted gel-forming mucus component Mucin-2 and stabilizes the colonic mucus layer
The colonic mucus layer is an organized system providing a physical barrier against pathogens and simultaneously harbouring the commensal flora. Here the authors report that transglutaminase 3 activity contributes to homeostasis of the colonic mucus layer and the lack of this enzymatic activity leads to increased susceptibility against DSS-induced colitis in mice.
- Jack D. A. Sharpen
- , Brendan Dolan
- & Christian V. Recktenwald
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Article
| Open AccessAminoacyl chain translocation catalysed by a type II thioesterase domain in an unusual non-ribosomal peptide synthetase
Non-Ribosomal Peptide Synthetases (NRPSs) are responsible for the construction of many types of natural products. Here the authors characterize a key type II thioesterase domain that sheds light on the chain translocation processes of legonmycin NRPSs.
- Shan Wang
- , William D. G. Brittain
- & Hai Deng
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Article
| Open AccessThe catalytic activity of TCPTP is auto-regulated by its intrinsically disordered tail and activated by Integrin alpha-1
TCPTP is a non-receptor type protein tyrosine phosphatase involved in various signalling pathways. Here, the authors provide structural insights into TCPTP activation, showing that TCPTP is inhibited by its C-terminal tail, which can be displaced by the cytosolic tail of integrin-α1, leading to activation.
- Jai Prakash Singh
- , Yang Li
- & Tzu-Ching Meng
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Article
| Open AccessConformational changes in Lassa virus L protein associated with promoter binding and RNA synthesis activity
The L protein of segmented, negative strand RNA viruses contains the RNA-dependent RNA polymerase essential for virus amplification. Here, the authors report cryoEM structures of the Lassa virus L protein in active, RNA-bound states, and provide mechanistic insights.
- Tomas Kouba
- , Dominik Vogel
- & Stephen Cusack
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Article
| Open AccessStructural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites
Microbial DNA glycosylases associated with the biosynthesis of DNA-damaging antibiotics have evolved self-resistance for their cognate natural products. Here, the authors provide evidence that cellular self-resistance is enabled by reduced affinity of the glycosylases for the excision products of the corresponding DNA lesions.
- Elwood A. Mullins
- , Jonathan Dorival
- & Brandt F. Eichman
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Article
| Open AccessHelicobacter pylori FabX contains a [4Fe-4S] cluster essential for unsaturated fatty acid synthesis
Helicobacter pylori FabX, a dehydrogenase/isomerase flavoprotein, is required for unsaturated fatty acid synthesis. Here, the authors characterize FabX substrate recognition and catalytic mechanism, and reveal that it contains an atypical [4Fe-4S] cluster, which is essential and participates in the catalytic cycle.
- Jiashen Zhou
- , Lin Zhang
- & Liang Zhang
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Article
| Open AccessCryo-EM snapshots of a native lysate provide structural insights into a metabolon-embedded transacetylase reaction
How is acetyl-CoA produced in the context of the endogenous, eukaryotic pyruvate dehydrogenase complex metabolon? Here the authors dissect the embedded transacetylase reaction through biochemical, cryo-EM, HADDOCKing and molecular dynamics methods.
- Christian Tüting
- , Fotis L. Kyrilis
- & Panagiotis L. Kastritis
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Article
| Open AccessAGPAT2 interaction with CDP-diacylglycerol synthases promotes the flux of fatty acids through the CDP-diacylglycerol pathway
AGPATs (1-acylglycerol-3-phosphate O-acyltransferases) catalyze the acylation of lysophosphatidic acid to form phosphatidic acid (PA), a key step in the synthesis of all glycerolipids. Here, the authors show that AGPAT2 and CDP-DAG synthases (CDS1 and CDS2) form functional complexes that promote further conversion of PA along the CDP-DAG pathway of phospholipid synthesis.
- Hoi Yin Mak
- , Qian Ouyang
- & Hongyuan Yang
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Article
| Open AccessCrystal structures of the elusive Rhizobium etli l-asparaginase reveal a peculiar active site
L-asparaginases catalyse the hydrolysis of L-asparagine to L-aspartic acid and ammonia. Here, the authors present high resolution crystal structures of Rhizobium etli L-asparaginase that contains a Zn2+ binding site without a catalytic role and discuss the catalytic mechanism of the enzyme.
- Joanna I. Loch
- , Barbara Imiolczyk
- & Mariusz Jaskolski
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Article
| Open AccessMechanism of actin-dependent activation of nucleotidyl cyclase toxins from bacterial human pathogens
The nucleotidyl cyclase toxin exoenzyme Y (ExoY), which is secreted by the human pathogens Pseudomonas aeruginosa and Vibrio vulnificus is activated by actin. Here, the authors present the cryo-EM structures of PaExoY bound to F-actin and VvExoY in complex with G-actin-profilin. These structures together with molecular dynamics simulations and enzymatic assays provide insights into the activation mechanism for both bacterial cyclase toxin families that interact with either F- or G-actin.
- Alexander Belyy
- , Felipe Merino
- & Stefan Raunser
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Article
| Open AccessCryo-EM structure provides insights into the dimer arrangement of the O-linked β-N-acetylglucosamine transferase OGT
The modification of proteins with O-linked β-N-acetylglucosamine (OGlcNAc) plays roles in regulation of numerous cellular functions while incorrect O-GlcNAcylation patterns are linked to disease. Here, the authors report a cryo-EM structure of full-length O-GlcNAc transferase (OGT), the only enzyme responsible for O-GlcNAcylation.
- Richard W. Meek
- , James N. Blaza
- & Gideon J. Davies