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| Open AccessThe synthetic NLR RGA5HMA5 requires multiple interfaces within and outside the integrated domain for effector recognition
An engineered sensor NLR RGA5HMA5 carrying multiple resurfaced interfaces was generated to confer complete resistance to the rice blast fungus strains expressing the non-corresponding effector AVR-PikD, paving a way to broaden the resistance spectra of NLRs.
- Xin Zhang
- , Yang Liu
- & You-Liang Peng
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Article
| Open AccessStructural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes
UAP56 is an important factor in the TREX complex, which is responsible for mRNA export. Here the authors show that the closely related RNA helicases, UAP56 and URH49, exhibit different three-dimensional structures due to one amino acid change. Accordingly, they form distinct apo-complexes and function in the nuclear export of specific target mRNAs.
- Ken-ichi Fujita
- , Misa Ito
- & Seiji Masuda
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Article
| Open AccessDisordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners
Here, the authors investigate the maturation of human respiratory Complex II, uncovering two metastable intermediates of maturation which suggest changes in intrinsic disorder ensure that the assembly steps occur in the correct sequence.
- Pankaj Sharma
- , Elena Maklashina
- & T. M. Iverson
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Article
| Open AccessMultiple redox switches of the SARS-CoV-2 main protease in vitro provide opportunities for drug design
Here the authors demonstrate that the SARS-CoV-2 main protease (Mpro) is subject to redox regulation in vitro, reversibly switching between the enzymatically active dimer and the functionally dormant monomer through redox modifications of cysteine residues.
- Lisa-Marie Funk
- , Gereon Poschmann
- & Kai Tittmann
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Article
| Open AccessConformational coupling of the sialic acid TRAP transporter HiSiaQM with its substrate binding protein HiSiaP
Tripartite ATP-independent periplasmic (TRAP) transporters use an extra substrate binding protein to transport a variety of substrates in bacteria and archaea. Here the authors use a disulfide engineering approach to lock the TRAP transporter HiSiaPQM from H. influenzae in different conformational states for characterisation.
- Martin F. Peter
- , Jan A. Ruland
- & Gregor Hagelueken
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Article
| Open AccessTail-tape-fused virion and non-virion RNA polymerases of a thermophilic virus with an extremely long tail
The authors describe the structure and function of two evolutionarily diverged RNA polymerases of a thermophilic phage. One of the polymerases is fused to the phage tape measure protein, a virion component dictating the length of the phage tail.
- Anastasiia Chaban
- , Leonid Minakhin
- & Maria L. Sokolova
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Article
| Open AccessDiverse array of neutralizing antibodies elicited upon Spike Ferritin Nanoparticle vaccination in rhesus macaques
An adjuvanted SARS-CoV-2 spike-ferritin nanoparticle vaccine can elicit antibodies with relatively broad sarbecovirus activity in non-human primates. Here, the authors isolate and structurally characterize several monoclonal antibodies providing insights into the targeted epitopes and broad reactivity.
- Rajeshwer S. Sankhala
- , Kerri G. Lal
- & M. Gordon Joyce
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Article
| Open AccessAvapritinib-based SAR studies unveil a binding pocket in KIT and PDGFRA
Avapritinib, a potent inhibitor, offers hope for D842V-mutant GIST patients with high response rates; however, resistance and side effects remain challenges. Here, crystal structures shed light on this and reveal a Gα-pocket for drug development.
- A. Teuber
- , T. Schulz
- & D. Rauh
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Article
| Open AccessStructural insights into the regulation, ligand recognition, and oligomerization of bacterial STING
Here the authors present the crystal structure of a bacterial STING. The structure shows that bacterial STING can modulate immune responses by forming anti-parallel dimers or, in certain species, through the presence of a long lid.
- Mei-Hui Hou
- , Yu-Chuan Wang
- & Yeh Chen
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Article
| Open AccessThe Mycobacterium tuberculosis methyltransferase Rv2067c manipulates host epigenetic programming to promote its own survival
Singh et al. show how the M. tuberculosis methyltransferase Rv2067c outsmarts host epigenetic machinery by methylating histone H3 prior to its assembly into nucleosomes, thereby ensuring the pathogen’s intracellular survival/success.
- Prakruti R. Singh
- , Venkatareddy Dadireddy
- & Valakunja Nagaraja
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Article
| Open AccessAutoregulation of the LIM kinases by their PDZ domain
LIM domain kinases are key regulators of cofilin and consequently actin severing. Here, the authors show that the LIMK PDZ domain is important for autoregulation using a conserved surface distal to the canonical PDZ-binding cleft.
- Gabriela Casanova-Sepúlveda
- , Joel A. Sexton
- & Titus J. Boggon
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Article
| Open AccessA DARPin promotes faster onset of botulinum neurotoxin A1 action
Botulinum neurotoxins (BoNTs), the causative agents of the disease botulism, are potent biological toxins. Here the authors use Designed Ankyrin Repeat Proteins (DARPins) to probe BoNT structure and function: DARPin-F5 that completely blocks SNAP25 substrate cleavage by BoNT/A1 in vitro was identified.
- Oneda Leka
- , Yufan Wu
- & Richard A. Kammerer
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Article
| Open AccessA single C-terminal residue controls SARS-CoV-2 spike trafficking and incorporation into VLPs
Dey et al. use structure-function methods to show that partial mimicry of the coatomer-binding motif in the SARS-CoV-2 spike is crucial for its release post coatomer-dependent delivery, thus ensuring optimal spike fusogenicity and VLP incorporation.
- Debajit Dey
- , Enya Qing
- & S. Saif Hasan
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Article
| Open AccessZNF524 directly interacts with telomeric DNA and supports telomere integrity
ZNF524 is a newly described protein that binds to telomeres, the ends of linear chromosomes. ZNF524 promotes the presence of two members of the shelterin complex, TRF2/RAP1, at telomeres, and prevents genomic instability.
- Hanna Braun
- , Ziyan Xu
- & Dennis Kappei
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Article
| Open AccessStructural and thermodynamic insights into antibody light chain tetramer formation through 3D domain swapping
Atomic-level structural examinations of antibody light chain aggregates are sparse. Here, the authors find an antibody light chain that maintains an equilibrium between monomeric and tetrameric states and show with its 3D structure that it engages in 3D domain swapping within its variable region.
- Takahiro Sakai
- , Tsuyoshi Mashima
- & Shun Hirota
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Article
| Open AccessA multi-reservoir extruder for time-resolved serial protein crystallography and compound screening at X-ray free-electron lasers
Protein serial crystallography at X-ray free-electron lasers (XFELs) is a powerful technique for structure determination. Here, authors present a device for sample delivery designed to abate challenges to non-specialists allowing for compound screening.
- Maximilian Wranik
- , Michal W. Kepa
- & Jörg Standfuss
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Article
| Open AccessStructural basis of a redox-dependent conformational switch that regulates the stress kinase p38α
p38α is a kinase that regulates many cellular processes. Here authors report that redox fluctuations induce conformational changes to fine-tune the p38α activity beyond its activation loop phosphorylation.
- Joan Pous
- , Blazej Baginski
- & Maria J. Macias
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Article
| Open AccessPyroptosis inhibiting nanobodies block Gasdermin D pore formation
Pyroptosis has been implicated in many diseases with aberrant inflammation. Here, Kopp et al. characterize single-chain nanobodies targeting the human gasdermin D protein as tools to inhibit pyroptosis.
- Anja Kopp
- , Gregor Hagelueken
- & Matthias Geyer
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Article
| Open AccessIlluminating the mechanism and allosteric behavior of NanoLuc luciferase
NanoLuc luciferase is a popular bioluminescent enzyme, but the molecular details of its mechanism of action on luciferins such as coelenterazine remained elusive. Here the authors use, protein crystal structures and biochemical analyses to provide an atomistic description of its catalytic mechanism and allosteric behaviour.
- Michal Nemergut
- , Daniel Pluskal
- & Martin Marek
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Article
| Open AccessDiscovery of a non-canonical prototype long-chain monoacylglycerol lipase through a structure-based endogenous reaction intermediate complex
Here, the authors present the structure of an orphan lipase in complex with an endogenous C18 monoacylglycerol ester reaction intermediate derived from the expression host, which along with enzymatic assays enabled functional assignment as a prototypical long-chain monoacylglycerol lipase.
- Nikos Pinotsis
- , Anna Krüger
- & Matthias Wilmanns
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Article
| Open AccessStochastic chain termination in bacterial pilus assembly
Adhesive type-1 pili from Escherichia coli are filamentous protein complexes consisting of a short tip and a long rod formed by up to several thousand copies of a major subunit. Here, Giese et al. reconstitute the entire type-1 pilus rod assembly reaction in vitro, using all constituent protein subunits, and identify a subunit that acts as an irreversible assembly terminator.
- Christoph Giese
- , Chasper Puorger
- & Rudi Glockshuber
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Article
| Open AccessStructure-based discovery of dual pathway inhibitors for SARS-CoV-2 entry
TMPRSS2 and CTSL/CTSB, host proteases that facilitate SARS-CoV-2 entry, are promising drug targets. Here the authors simultaneously inhibit these host proteases and see synergistic antiviral effects, offering a broad-spectrum intervention against SARS-CoV-2 variants.
- Haofeng Wang
- , Qi Yang
- & Haitao Yang
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Article
| Open AccessStructures of the interleukin 11 signalling complex reveal gp130 dynamics and the inhibitory mechanism of a cytokine variant
Interleukin (IL-)11 is a signaling protein that plays key roles in several human diseases. Here the authors describe structures of IL-11 in complex with its receptors and determine the molecular mechanisms through which a variant of IL-11 inhibits signalling, opening avenues for therapeutic development.
- Riley D. Metcalfe
- , Eric Hanssen
- & Michael D. W. Griffin
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Article
| Open AccessThe structural and functional investigation into an unusual nitrile synthase
The nitrile synthase AetD is a crucial component in the biosynthetic pathway of neurotoxin aetokthonotoxin (AETX). Here, the authors solved crystal structures of AetD in complex with different substrates, revealing that AetD represents a new type of HO-like diiron enzyme and the possibility of expanding its substrate spectrum.
- Hao Li
- , Jian-Wen Huang
- & Chun-Chi Chen
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Article
| Open AccessUnconventional structure and mechanisms for membrane interaction and translocation of the NF-κB-targeting toxin AIP56
Structural and functional characterization of an NF-κB-targeting bacterial toxin reveals an unconventional structure and mechanisms of membrane interaction and translocation.
- Johnny Lisboa
- , Cassilda Pereira
- & Nuno M. S. dos Santos
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Article
| Open AccessMechanistic insights into glycoside 3-oxidases involved in C-glycoside metabolism in soil microorganisms
Integrated experimental and computational approaches reveal functional and structural details of a key catabolic enzyme that oxidizes recalcitrant C-glycosides, abundant and biologically significant natural molecules, before deglycosylation.
- André Taborda
- , Tomás Frazão
- & Lígia O. Martins
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Article
| Open AccessIntra- and inter-molecular regulation by intrinsically-disordered regions governs PUF protein RNA binding
FBF-2 and LST-1 repress gld-1 mRNA expression to maintain C. elegans germline stem cells. The authors show that an intrinsically-disordered region of FBF-2 autoinhibits its RNA binding. LST-1 antagonizes this interaction to promote RNA binding.
- Chen Qiu
- , Zihan Zhang
- & Traci M. Tanaka Hall
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Article
| Open AccessFunctional and structural diversity in deubiquitinases of the Chlamydia-like bacterium Simkania negevensis
Intracellular bacteria use deubiquitinase effectors to avoid being targeted for autophagic clearance. The authors show that the Chlamydia-like bacterium Simkania negevensis encodes an unusually broad range of these enzymes, including members that specifically target linear and K6-linked ubiquitin chains.
- Vanessa Boll
- , Thomas Hermanns
- & Kay Hofmann
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Article
| Open AccessStructures of the DarR transcription regulator reveal unique modes of second messenger and DNA binding
The molecular basis for 2nd messenger binding to the TetR family regulator (TFR), DarR, is unknown. Here the authors obtain DarR structures bound to adenine 2nd messengers and DNA, revealing both a new TFR allosteric binding site and DNA binding mode.
- Maria A. Schumacher
- , Nicholas Lent
- & Raul Salinas
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Article
| Open AccessMechanism of selective recognition of Lys48-linked polyubiquitin by macrocyclic peptide inhibitors of proteasomal degradation
Macrocyclic peptides were recently discovered as potent modulators of ubiquitin-mediated cellular signaling pathways. Here the authors used multidisciplinary approach to uncover how macrocyclic peptides that inhibit proteasomal degradation selectively recognize long Lys48-linked polyubiquitin chains.
- Betsegaw Lemma
- , Di Zhang
- & David Fushman
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Article
| Open AccessInadequate structural constraint on Fab approach rather than paratope elicitation limits HIV-1 MPER vaccine utility
It is still unclear why HIV-1 vaccines targeting MPER induce antibodies that fail to bind HIV. Here, the authors show that antibodies targeting membrane-proximal linear epitopes of virion spike proteins must generate relevant antibody paratopes and approach angles to ligate their quarry in a topologically restricted site.
- Kemin Tan
- , Junjian Chen
- & Mikyung Kim
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Article
| Open AccessEnzymatic β-elimination in natural product O- and C-glycoside deglycosylation
Biological degradation of glycosides involves, alongside hydrolysis, β-elimination for glycosidic bond cleavage. Here, the authors report an O-glycoside β-eliminase from Agrobacterium tumefaciens that converts the C3-oxidized O-β-d-glucoside of phloretin into the aglycone and the 2-hydroxy-3-keto-d-glycal elimination product, and suggest convergent evolution of β-eliminase active sites for the cleavage of natural product 3-keto-O-glycosides.
- Johannes Bitter
- , Martin Pfeiffer
- & Bernd Nidetzky
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Article
| Open AccessStructure and function of the EA1 surface layer of Bacillus anthracis
S-layers form continuous protein lattices on the surface of bacteria. Here, authors use S-layer depolymerizing nanobodies to solve the structure of the EA1 S-layer in the pathogen Bacillus anthracis and show its role as cell wall supportive structure”
- Adrià Sogues
- , Antonella Fioravanti
- & Han Remaut
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Article
| Open AccessRecognition and reprogramming of E3 ubiquitin ligase surfaces by α-helical peptides
Identification of molecules that induce novel interactions between proteins has been limited by the complexity of rationally designing interactions. The authors report a method to discover molecular glue-like “trimerizers” based on α-helically constrained peptides that can co-opt the surfaces of E3 ubiquitin ligases to bind therapeutically important proteins.
- Olena S. Tokareva
- , Kunhua Li
- & John H. McGee
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Article
| Open AccessMechanism of substrate hydrolysis by the human nucleotide pool sanitiser DNPH1
Inactivation of DNPH1 leads to hmdU incorporation into DNA, sensitising BRCA-deficient cells to PARP inhibitors. Crystal structures of DNPH1 bound to hmdU monophosphate reveal a two-step mechanism for hydrolysis via a glycosyl-enzyme intermediate.
- Neil J. Rzechorzek
- , Simone Kunzelmann
- & Stephen C. West
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Article
| Open AccessPhosphorylation-dependent pseudokinase domain dimerization drives full-length MLKL oligomerization
How the necroptosis executioner, MLKL, converts to a killer form has been mysterious. Here, authors show RIPK3-mediated phosphorylation of human MLKL is the cue for pseudokinase domain dimerization before assembly of pro-necroptotic MLKL tetramers.
- Yanxiang Meng
- , Sarah E. Garnish
- & James M. Murphy
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Article
| Open AccessDe novo design of knotted tandem repeat proteins
This study reports the successful de novo design of a trefoil knotted protein fold for which the crystal structure agrees closely with the intended trefoil knot topology.
- Lindsey A. Doyle
- , Brittany Takushi
- & Philip Bradley
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Article
| Open AccessHow myosin VI traps its off-state, is activated and dimerizes
Canon et al. offer insights into the auto-inhibition and activation of the minus-end directed motor myosin VI. The work highlights how differential relief of auto-inhibition allows for fine control of myosin VI activity in vivo.
- Louise Canon
- , Carlos Kikuti
- & Anne Houdusse
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Article
| Open AccessInsights into the missing apiosylation step in flavonoid apiosides biosynthesis of Leguminosae plants
Apiosides are plant bioactive natural products containing apiose, but the details of the key apiosylation reaction in their biosynthesis are missing. Here, the authors identify the apiosyltransferase GuApiGT that could efficiently catalyze 2″-O-apiosylation of flavonoid glycosides, solve its crystal structure and obtain mutants with altered sugar selectivity.
- Hao-Tian Wang
- , Zi-Long Wang
- & Min Ye
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Article
| Open AccessLactate dehydrogenase D is a general dehydrogenase for D-2-hydroxyacids and is associated with D-lactic acidosis
Currently the structure and biological function of Lactate Dehydrogenase D (LDHD) are unclear. Here the authors report the structure of LDHD bound with various ligands and show that LDHD is a general dehydrogenase for D-2-hydroxyacids with small to moderate-size hydrophobic moieties and investigate loss-of-function mutations that play an important role in D-lactic acidosis.
- Shan Jin
- , Xingchen Chen
- & Jianping Ding
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Article
| Open AccessAn allosteric switch between the activation loop and a c-terminal palindromic phospho-motif controls c-Src function
Protein kinase transition between different conformational states is controlled by autophosphorylation. Here, the authors demonstrate that the c-terminal Tyr530 is a de facto c-Src autophosphorylation site and identify a critical c-terminal palindromic phospho-motif that controls the interplay between substrate and enzyme-acting kinases during autophosphorylation.
- Hipólito Nicolás Cuesta-Hernández
- , Julia Contreras
- & Iván Plaza-Menacho
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Article
| Open AccessA single nanobody neutralizes multiple epochally evolving human noroviruses by modulating capsid plasticity
GII.4 human noroviruses cause pandemic gastroenteritis and undergo epochal evolution. This study shows that a single Llama-derived nanobody neutralizes multiple GII.4 variants using a mechanism by targeting capsid plasticity.
- Wilhelm Salmen
- , Liya Hu
- & B. V. Venkataram Prasad
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Article
| Open AccessStructural basis for the unique molecular properties of broad-range phospholipase C from Listeria monocytogenes
The bacterium Listeria monocytogenes possesses two major virulence factors, broad-range phospholipase C (LmPC-PLC) and the pore-forming toxin listeriolysin O (LLO). Here, authors perform structural and biochemical analysis of LmPC-PLC and show that unique structural features enable self-regulation of its enzymatic activity and positive synergy with the pore-forming toxin listeriolysin O.
- Nejc Petrišič
- , Maksimiljan Adamek
- & Marjetka Podobnik
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Article
| Open AccessStructural basis for triacylglyceride extraction from mycobacterial inner membrane by MFS transporter Rv1410
Triacylglycerides help to secure the impermeability of mycobacterial cell envelope to some drugs. Here, authors solve the structure of the triacylglyceride transporter Rv1410 and proposed a molecular mechanism for triacylglyceride extraction.
- Sille Remm
- , Dario De Vecchis
- & Markus A. Seeger
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Article
| Open AccessMolecular mechanism of decision-making in glycosaminoglycan biosynthesis
Heparan sulfate (HS) and chondroitin sulfate (CS) are different glycosaminoglycan chains that are attached to core proteins via the same linker tetrasaccharide, and it was unclear how core proteins are specifically modified with HS or CS. Here, the authors determine that the CS-initiating glycosyltransferase CSGALNACT2 is promiscuous, whereas the HS-initiating glycosyltransferase EXTL3 selects only certain core proteins for modification.
- Douglas Sammon
- , Anja Krueger
- & Erhard Hohenester
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Article
| Open AccessStructure of full-length cobalamin-dependent methionine synthase and cofactor loading captured in crystallo
Methionine synthase (MS) harnesses B12 and flexibility to catalyze three different reactions on one protein. The full-length structure of MS yields insights into a protein that epitomizes controlled dynamics to dictate chemical outcome.
- Johnny Mendoza
- , Meredith Purchal
- & Markos Koutmos
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Article
| Open AccessStructure-guided inhibition of the cancer DNA-mutating enzyme APOBEC3A
APOBEC3A mutates its host DNA in human cancers to evolve drug resistance. Modified-DNA inhibitors suppress this mutagenic activity in cells, suggesting use as conjuvants in anti-cancer therapies. Here the authors reveal structural insights into how these inhibitors bind APOBEC3A.
- Stefan Harjes
- , Harikrishnan M. Kurup
- & Geoffrey B. Jameson
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Article
| Open AccessStructure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2
SH2 domains are challenging to target using small molecules. Here, the authors develop phosphotyrosine-based covalent ligands of the E3 ligase SOCS2 using structure-based design. A pro-drug approach yields cell active inhibitors that block SOCS2 substrate recruitment.
- Sarath Ramachandran
- , Nikolai Makukhin
- & Alessio Ciulli
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Article
| Open AccessTriepoxide formation by a flavin-dependent monooxygenase in monensin biosynthesis
MonCI, a flavin-dependent monooxygenase, transforms all three C = C groups in the polyene substrate into epoxides during monensin A biosynthesis. Here, the authors present the structural basis for this enzyme’s regio- and stereoselective epoxidation activity.
- Qian Wang
- , Ning Liu
- & Chu-Young Kim