Phaser crystallographic software

Structural basis for the RNA binding properties of mouse IGF2BP3

IGF2BP family proteins (IGF2BPs) contain six tandem RNA-binding domains (RBDs), resulting in highly complex RNA binding properties. Dissecting how IGF2BPs recognize their RNA targets is essential for understanding their regulatory roles in gene expression. Here, we have determined the crystal structures of mouse IGF2BP3 constructs complexed with different RNA substrates. Our structures reveal that the IGF2BP3-RRM12 domains can recognize CA-rich elements up to 5-nt in length, mainly through RRM1. We also captured the antiparallel RNA-binding mode of the IGF2BP3-KH12 domains, with five nucleotides bound by KH1 and two nucleotides bound by KH2. Furthermore, our structural and biochemical studies suggest that the IGF2BP3-KH12 domains could recognize the "zipcode" RNA element within the β-actin mRNA. Finally, we analyzed the similarities and differences of the RNA-binding properties between the KH12 and KH34. Our studies provide structural insights into RNA target recognition by mouse IGF2BP3.

LTD coordinates chlorophyll biosynthesis and LIGHT-HARVESTING CHLOROPHYLL A/B-BINDING PROTEIN transport

Chlorophyll biosynthesis must be tightly coupled to light-harvesting chlorophyll a/b-binding protein (LHCP) biogenesis, as free chlorophyll and its precursors are phototoxic. However, precisely how these 2 processes are coordinated in Arabidopsis (Arabidopsis thaliana) remains elusive. Our previous studies demonstrated the role of LHCP TRANSLOCATION DEFECT (LTD) in delivering LHCPs to the chloroplast via the signal recognition particle-dependent pathway. Here, we show that LTD interacts with and stabilizes the chlorophyll biosynthesis enzymes Mg-protoporphyrin methyltransferase and Mg-protoporphyrin monomethylester (MgPME) cyclase, maintaining their activity. We also demonstrate the direct binding of LTD to MgPME, and through crystal structure analysis, we show that the groove of the LTD dimer is critical for MgPME binding. Thus, we propose that LTD transfers MgPME from Mg-protoporphyrin methyltransferase to the MgPME cyclase. These results elucidate a role for LTD in synchronizing chlorophyll biosynthesis with LHCP transport to ensure the correct insertion of chlorophylls into LHCPs.

Protein ligation for the assembly and study of nonribosomal peptide synthetase megaenzymes

Nonribosomal peptide synthetases (NRPSs) are biosynthetic enzymes found in bacteria and fungi, that synthesize a plethora of pharmaceutically relevant compounds. NRPSs consist of repeating sets of functional domains called modules, and each module is responsible for the incorporation of a single amino acid to the growing peptidyl intermediate. The synthetic logic of an NRPS resembles an assembly line, with growing biosynthesis intermediates covalently attached to the prosthetic 4'-phosphopantetheine (ppant) moieties of T (thiolation or transfer) domains for shuttling within and between modules. Therefore, NRPSs must have each T domain phosphopantetheinylated to be functional, and host organisms encode ppant transferases that affix ppant to T domains. Ppant transferases can be promiscuous with respect to the T domain substrate and with respect to chemical modifications of the ppant thiol, which has been a useful characteristic for study of megaenzymes and other systems. However, defined studies of multimodular megaenzymes, where different analogs are required to be affixed to different T domains within the same multimodular protein, are hindered by this promiscuity. Study of NRPS peptide bond formation, for which two T domains simultaneously deliver substrates to the condensation domain, is a prime example where one would want two T domains bearing different acyl/peptidyl groups. Here, we report a strategy where two NRPS modules that are normally part of the same protein are expressed as separate constructs, modified separately with different acyl-ppants, and then ligated together by sortase A of Staphylococcus aureus or asparaginyl endopeptidase 1 of Oldenlandia affinis (OaAEP1). We assessed various reaction conditions to optimize the ligation reactions and maximize the yield of the complex of interest. Finally, we apply this method in large scale and show it allows the complex built by OaAEP1-mediated ligation to be characterized by X-ray crystallography.

Ancestral proteins trace the emergence of substrate specificity and oligomerization within bacterial DEDDy dinucleases

Nucleases play a crucial role in bacterial physiology, influencing processes such as DNA repair, genome maintenance, and host-pathogen interactions. We recently identified a class of nucleases, diDNases, which are encoded on mobile genetic elements and homologous to the house-keeping nanoRNase C (NrnC). Despite their shared structural fold, diDNases and NrnC orthologs exhibit differences. DiDNases form dimers and preferably cleave DNA dinucleotides, whereas NrnC homologs assemble into octamers that do not discriminate between RNA or DNA dinucleotides. Here, we investigate the evolutionary divergence of these enzymes using ancestral sequence reconstruction. Our results show that both diDNases and NrnC orthologs originated from a dimeric ancestor with intermediate substrate preferences. Structural analyses of ancestral and extant dinucleases provide a molecular rational for how gradual changes in conformation gave rise to substrate preferences, oligomeric state, and catalytic efficiency of these related, yet distinct enzyme clades. These findings provide insights into how small structural modifications enable large-scale changes in molecular assembly and functional specialization harnessing a conserved protein fold. In addition, the preference of the early ancestors for DNA dinucleotides and preservation of this activity in all extant enzymes strongly argues for a biological function of DNA dinucleotides.

Nasal delivery of secretory IgA confers enhanced neutralizing activity against Omicron variants compared to its IgG counterpart

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its multiple variants continue to spread worldwide, causing respiratory symptoms primarily through mucosal infection. The mucosa serves as the primary barrier against viral entry, in which secretory immunoglobulin A (sIgA) plays a critical role in preventing infection. Here, we engineered and characterized a neutralizing monoclonal antibody, ZW2G10, in IgG, monomeric, dimeric, secretory IgA1, and IgA2 formats. All seven forms of the ZW2G10 antibody showed similar thermal stability. sIgA, especially sIgA1, displayed enhanced neutralizing activity against Omicron-lineage BA.2.75, BA.2.76 and BA.4/5 pseudoviruses compared to IgG. Nasal administration of sIgA1 conferred robust protection against the BA.2.76 pseudovirus in ACE2 transgenic mice, and its protective efficacy was superior to that of IgG. The crystal structure of Omicron receptor binding domain (RBD) and ZW2G10 antibody fragment (Fab) complex revealed that ZW2G10 had no clashes with ACE2. Thus, nasal administration of sIgA may serve as a promising tool for the prevention and treatment of Omicron infection.

Identification and Protein Engineering of Galactosidases for the Conversion of Blood Type B to Blood Type O

The supply of blood products such as red blood cells poses a challenge due to rising demand and declining donor numbers. Careful matching of blood products of different types is required. Only type O of the blood types A, B, AB and O can be received by any patient without transfusion incompatibilities. Therefore, O-type blood can be considered "universal blood" and is especially needed in emergency situations. In this study, we focused on the conversion of the B antigen by enzymatic deglycosylation to generate the H antigen determining O-type blood. For this, we characterized several previously unstudied α-1,3-galactosidases belonging to the GH110 family. Our findings revealed that the α-1,3-galactosidase from Pedobacter panaciterrae (PpaGal) exhibits superior efficiency compared to previously described galactosidases. We further increased the activity of PpaGal by 2.5-fold using site-directed mutagenesis. Moreover, we solved two crystal structures of PpaGal, one in the apo-state and another in complex with d-galactose. The combination of our mutagenesis study with the solved crystal structures provides valuable information to guide further optimization of PpaGal or other B antigen converting enzymes paving the way for the easier production of universal blood from B-type blood.

The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulates n-alkane degradation in Pseudomonas aeruginosa SJTD-1

Transmembrane alkane monooxygenase (AlkB)-type monooxygenases, especially AlkB2 monooxygenases, are crucial for aerobic degradation of the medium-to-long-chain n-alkanes in hydrocarbon-utilizing microorganisms. In this study, we identified a GntR/VanR transcription regulator AlkR of Pseudomonas aeruginosa SJTD-1 involved in the negative regulation of AlkB2 and deciphered its nature of DNA binding and ligand release. The deletion of alkR enhanced the transcription levels of the alkB2 gene and the utilization efficiency of the medium-to-long-chain n-alkanes by strain SJTD-1. The dimer of AlkR recognizes and binds to a conserved palindromic motif in the promoter of the alkB2 gene, and structural symmetry is vital for DNA binding and transcription repression. The long-chain fatty acyl coenzyme A compounds can release AlkR and stimulate transcription of alkB2, reflecting the effect of alkane catabolic metabolites. Structural insights unveiled that the arginine residues and scaffold residues of AlkR are critical for DNA binding. Further bioinformatics analysis of AlkR revealed the widespread VanR-AlkB couples distributed in Pseudomonadaceae with high conservation in the sequences of functional genes and intergenic regions, highlighting a conserved regulatory pattern for n-alkane utilization across this family. These findings demonstrate the regulatory mechanism and structural basis of GntR/VanR transcription regulators in modulating n-alkane biodegradation and provide valuable insights in improving the bioremediation efficiency of hydrocarbon pollution.

Crystal structures of forty- and seventy-one-substitution variants of hydroxynitrile lyase from rubber tree

The α/β-hydrolase fold family contains mostly esterases but includes other enzymes such as hydroxynitrile lyase from Hevea brasiliensis (rubber tree, Hb HNL). Hb HNL shares 44% sequence identity and a Ser-His-Asp catalytic triad with esterase SABP2 (salicylic acid binding protein 2 from Nicotiana tabacum (tobacco)). To identify how large a region within Hb HNL influences the positions of the catalytic residues, we created variants where increasingly large regions surrounding the substrate-binding site had identical amino acid sequences to those in SABP2. Variant HNL40 contains 40 mutations (two inserted amino acid residues, 38 substitutions), shares 59% sequence identity with SABP2, and is identical in sequence to SABP2 within 10 Å of the substrate-binding site. Variant HNL71 contains 31 additional substitutions for a total of 71 changes (two insertions, 69 substitutions) and shares 71% sequence identity with SABP2. The sequences within 14 Å of the substrate-binding site are identical in SABP2 and HNL71. The crystal structures of HNL40 and HNL71 show that the positions of main chain Cɑ atoms move from their positions in Hb HNL to more closely match those in SABP2 (RMSD = 0.51 Å over 235 Cɑ atoms for HNL40, 0.41 Å over 219 Cɑ atoms for HNL71) and even more closely in the region within 10 Å of the substrate-binding site (RMSD = 0.38 Å over 58 Cɑ atoms for HNL40, 0.28 Å over 53 Cɑ atoms for HNL71). The pattern of tunnels in HNL40 and HNL71 are similar to each other and intermediate between the pattern in Hb HNL and SABP2.

Synopsis

Variants HNL40 and HNL71 of hydroxynitrile lyase from Hevea brasiliensis contain 40 and 71 mutations, respectively, to make regions surrounding the substrate-binding site identical in sequence to esterase SABP2. X-ray structures reveal increasing similarities to SABP2 in HNL40 and HNL71. PDB reference: hydroxynitrile lyase from Hevea brasiliensis with forty mutations, 8SNI, hydroxynitrile lyase from Hevea brasiliensis with seventy-one mutations, 9CLR.

Structure and catalytic activity of a dihydrofolate reductase-like enzyme from Leptospira interrogans

A dihydrofolate reductase (DHFR)-like enzyme from Leptospira interrogans (LiDHFRL) was cloned and the recombinant protein was characterized. Sequence alignment suggested that the enzyme lacked the conserved catalytic residues found in DHFR. Indeed, LiDHFRL did not catalyze the reduction of dihydrofolate by either NADH or NADPH. X-ray crystallography revealed that LiDHFRL bound NADP(H) tightly, but its active site architecture was vastly different from that of Escherichia coli DHFR (EcDHFR) and other DHFRLs. Interestingly, vanillin could serve as a substrate for LiDHFRL, demonstrating that LiDHFRL is a functional enzyme. A putative vanillin binding mode was proposed.

Impact of Cancer-Associated PKM2 Mutations on Enzyme Activity and Allosteric Regulation: Structural and Functional Insights into Metabolic Reprogramming

Mammalian pyruvate kinase M2 (PKM2) is a key regulator of glycolysis and is highly expressed in proliferative tissues including tumors. Mutations in PKM2 have been identified in various cancers, but their effects on enzyme activity and regulation are not fully understood. This study investigates the structural and functional effects of cancer-associated PKM2 mutations on enzyme kinetics, allosteric regulation, and oligomerization. Using computational modeling, X-ray crystallography, and biochemical assays, we demonstrated how these mutations impact PKM2 activity, substrate binding, and allosteric activation via fructose-1,6-bisphosphate (FBP), contributing to altered enzyme function. In this study, we characterized four cancer-associated PKM2 mutations (P403A, C474S, R516C, and L144P) using computational, structural, and biochemical approaches. Computational modeling revealed disruptions in allosteric signaling pathways, particularly affecting the communication between regulatory sites and the active site. X-ray crystallography demonstrated local conformational changes in the hinge and FBP-binding regions, leading to a shift from the active tetrameric state to a less active dimeric state, particularly in the C474S and R516C mutants. The mutants exhibited reduced maximal velocity, reduced substrate affinity, and altered activation by the allosteric activator fructose-1,6-bisphosphate (FBP). Under alkaline pH conditions, mimicking the tumor microenvironment, these mutations further destabilized the PKM2 oligomeric state, favoring the formation of lower-order species. Our findings suggest that PKM2 is highly sensitive to mutations, and these alterations may contribute to metabolic reprogramming in cancer cells by impairing its enzymatic regulation.

Structural insights into the dual Ca2+-sensor-mediated activation of the PPEF phosphatase family

Serine/threonine-protein phosphatases with EF-hands (PPEFs) are a family of highly conserved proteins implicated in cancer and neuronal degeneration. The initially characterized member, Drosophila melanogaster retinal degeneration C (RDGC) contains a calmodulin (CaM)-interacting extended-IQ motif and a Ca2+-binding EF-like/EF-hand tandem. However, the molecular regulation of PPEF is poorly understood. In this study, we use cryogenic-electron microscopy to delineate the structures of the RDGC/CaM holoenzyme. In the absence of Ca2+, CaM and the EF-like/EF-hand tandem allow the extended-IQ motif to block substrate access to the catalytic sites, constituting an auto-inhibitory mechanism. Upon Ca2+ binding, CaM and the EF-like/EF-hand tandem drive drastic conformational changes in the extended-IQ motif to unlock the catalytic sites. This dual Ca2+-sensor-mediated activation is evolutionarily conserved in mammals. This study provides mechanistic insight into the molecular activation of PPEFs, paving the way for the development of therapeutic strategies for PPEF-related human diseases.

The crystal structures of apo and tryptophan-bound tryptophanyl-tRNA synthetase from Neisseria gonorrhoeae

Neisseria gonorrhoeae, the causative agent of the human disease gonorrhea, is the second most common sexually transmitted pathogen in the United States. Gonorrhea has a significantly high morbidity rate due to the ability of N. gonorrhoeae to rapidly develop antibiotic resistance. In this paper, crystal structures of tryptophanyl-tRNA synthetase (TrpRS) from N. gonorrhoeae (NgTrpRS) were determined in both its apo form and in complex with tryptophan. The structures reveal conserved HIGH and KMSKS motifs critical for ATP binding and catalysis, and highlight conformational changes in the active site upon tryptophan binding, including a methionine flip and the rearrangement of hydrogen-bonding residues. Structural alignments with human TrpRS isoforms demonstrate significant differences between the bacterial and human cytosolic forms, particularly in their active sites. While NgTrpRS and human mitochondrial TrpRS share conserved catalytic residues that are essential for binding tryptophan and indolmycin, the cytosolic TrpRS contains substitutions that introduce steric hindrance, limiting the binding of indolmycin. These results provide insight for the development of inhibitors targeting bacterial TrpRS without affecting the human mitochondrial or cytosolic isoforms, contributing to efforts to combat antibiotic-resistant N. gonorrhoeae infections.

Structural and functional characterization of the extended-diKH domain from the antiviral endoribonuclease KHNYN

Zinc finger antiviral protein (ZAP) binds CpG dinucleotides in viral RNA and targets them for decay. ZAP interacts with several cofactors to form the ZAP antiviral system, including KHNYN, a multidomain endoribonuclease required for ZAP-mediated RNA decay. However, it is unclear how the individual domains in KHNYN contribute to its activity. Here, we demonstrate that the KHNYN amino-terminal extended-diKH (ex-diKH) domain is required for antiviral activity and present its crystal structure. The structure belongs to a rare group of KH-containing domains, characterized by a noncanonical arrangement between two type 1 KH modules, with an additional helical bundle. N4BP1 is a KHNYN paralog with an ex-diKH domain that functionally complements the KHNYN ex-diKH domain. Interestingly, the ex-diKH domain structure is present in N4BP1-like proteins in lancelets, which are basal chordates, indicating that it is evolutionarily ancient. While many KH domains demonstrate RNA binding activity, biolayer interferometry and electrophoretic mobility shift assays indicate that the KHNYN ex-diKH domain does not bind RNA. Furthermore, residues required for canonical KH domains to bind RNA are not required for KHNYN antiviral activity. By contrast, an inter-KH domain cleft in KHNYN is a potential protein-protein interaction site, and mutations that eliminate arginine salt bridges at the edge of this cleft decrease KHNYN antiviral activity. This suggests that this domain could be a binding site for an unknown KHNYN cofactor.

Conformational flexibility of human ribokinase captured in seven crystal structures

d-ribose is a critical sugar substrate involved in the biosynthesis of nucleotides, amino acids, and cofactors, with its phosphorylation to ribose-5-phosphate by ribokinase (RK) constituting the initial step in its metabolism. RK is conserved across all domains of life, and its activity is significantly enhanced by monovalent metal (M+) ions, particularly K+, although the precise mechanism of this activation remains unclear. In this study, we present several crystal structures of human RK in both unliganded and substrate-bound states, offering detailed insights into its substrate binding process, reaction mechanism, and conformational changes throughout the catalytic cycle. Notably, bound ATP exhibited significant conformational flexibility in its triphosphate moiety, a feature shared with other RK homologues, suggesting that achieving a catalytically productive triphosphate configuration plays a key role in regulating enzyme activity. We also identified a unique conformational change in the M+ ion binding loop of human RK, specifically the flipping of the Gly306-Thr307 peptide plane, likely influenced by the ionic radius of the bound ion. These findings provide new insights into the RK reaction mechanism and its activation by M+ ions, paving the way for future investigations into the allosteric regulation of human RK and related sugar kinase enzymes.

Generation and characterization of neutralizing antibodies against M1R and B6R proteins of monkeypox virus

The global outbreak of monkeypox virus (MPXV), combined with the termination of smallpox vaccination and the lack of specific antiviral treatments, raises increasing concerns. The surface proteins M1R and B6R of MPXV are crucial for virus transmission and serve as key targets for vaccine development. In this study, a panel of human antibodies targeting M1R and B6R is isolated from a human antibody library using phage display technology. Among these antibodies, A138 against M1R and B026 against B6R show the most potent broad-spectrum neutralizing activities against MPXV and Vaccinia virus (VACV). When used in combination, A138 and B026 exhibit complementary neutralizing activity against both viruses in vitro. X-ray crystallography reveales that A138 binds to the loop regions of M1R, similar to the vulnerable epitope of 7D11 on VACV L1R. By contrast, A129 targets a more cryptic epitope, primarily comprising the β-strands of M1R. Moreover, prophylactic and therapeutic administration of A138 or B026 alone provides partial protection, while combining these two antibodies results in enhanced protection against VACV in male C57BL/6 mice. This study demonstrates of a dual-targeting strategy using two different components of the virion for the prevention and treatment of MPXV infection.

A multivalent engagement of ENL with MOZ

The epigenetic cofactor ENL (eleven-nineteen-leukemia) and the acetyltransferase MOZ (monocytic leukemia zinc finger) have vital roles in transcriptional regulation and are implicated in aggressive forms of leukemia. Here, we describe the mechanistic basis for the intertwined association of ENL and MOZ. Genomic analysis shows that ENL and MOZ co-occupy active promoters and that MOZ recruits ENL to its gene targets. Structural studies reveal a multivalent assembly of ENL at the intrinsically disordered region (IDR) of MOZ. While the extraterminal (ET) domain of ENL recognizes the canonical ET-binding motif in IDR, the YEATS domains of ENL and homologous AF9 bind to a set of acetylation sites in the MOZ IDR that are generated by the acetyltransferase CBP (CREB-binding protein). Our findings suggest a multifaceted acetylation-dependent and independent coupling of ENL, MOZ and CBP/p300, which may contribute to leukemogenic activities of the ENL-MOZ assembly and chromosomal translocations of ENL, MOZ and CBP/p300.

Apparent Reversal of Allosteric Response in Mycobacterium tuberculosis MenD Reveals Links to Half-of-Sites Reactivity

Redox-active molecules play critical roles in various biological functions, including cellular respiration. In bacterial electron transport chains, menaquinones serve as key electron carriers. The first committed enzyme in the menaquinone biosynthesis pathway of Mycobacterium tuberculosis (Mtb), MenD, is allosterically inhibited by 1,4-dihydroxy-2-naphthoic acid (DHNA), the first redox-active metabolite in the pathway. Structural asymmetries in Mtb-MenD suggest that this enzyme operates via a half-of-sites mechanism for catalysis. Here, we investigate the interplay between its catalytic and allosteric mechanisms. Using molecular dynamics (MD) simulations, mutagenesis, kinetic and binding assays, and structural analyses, we identified and characterised mutants of two residues, D141 and D306, involved in stabilising asymmetric conformations associated with allostery. These mutations had complex effects on Mtb-MenD's reaction kinetics, with the D306 mutants showing an apparent reversal of the allosteric response to DHNA. Our findings indicate that asymmetric active site conformations may facilitate optimal binding of cofactors and substrates, while the transition between alternating active site conformations is essential for the catalytic cycle. DHNA binding stabilises asymmetry in the tetramer, likely promoting the binding of cofactors, substrates, or reaction intermediates. However, DHNA interferes with the transition between alternating conformations, ultimately impairing turnover and catalytic cycling in Mtb-MenD.

Structural insights into CDF1 accumulation on the CONSTANS promoter via a plant-specific DNA-binding domain

DNA-binding with one-finger (Dof) proteins are a family of plant-specific transcription factors distinguished by the highly conserved Dof DNA-binding domain. Various members play crucial roles in diverse plant biological processes. However, it remains unclear how the Dof domain recognizes a restricted set of promoters for gene regulation by binding to just four nucleotides, AAAG/CTTT. Here we present the crystal structure of the Dof domain of CYCLING DOF FACTOR 1 (CDF1), a well-characterized Dof protein acting as a transcriptional repressor by binding to the CONSTANS promoter to regulate photoperiodic flowering, in complex with DNA containing two cis elements. The data reveal that the Dof domain exhibits a unique zinc ribbon fold that includes a three-stranded antiparallel β-sheet and a carboxy-terminal loop, enabling DNA recognition accompanied by directional expansion of the major groove. These features facilitate binding to contiguous target cis elements in a proper arrangement to effectively regulate gene expression.

Crystal Structure of a Thioredoxin-like Ferredoxin Encoded Within a Cobalamin Biosynthetic Operon of Rhodobacter capsulatus

Thioredoxin-like ferredoxin is a small homodimeric protein containing a [2Fe-2S] cluster in each monomer. It is only found in bacteria but its physiological function remains largely unknown. The cobalamin biosynthetic operon in the genome of the purple phototroph Rhodobacter capsulatus encodes a putative ferredoxin dubbed as CfrX. To characterize this protein, we cloned, expressed, purified, and crystalized the recombinant CfrX in the iron-sulfur cluster-bound state, and solved the structure at 2.1-Å resolution. Adopting a typical thioredoxin-like ferredoxin fold, a CfrX monomer binds one [2Fe-2S] cluster through four Cys residues located on two protruding loops. Unexpectedly, CfrX dimerizes in a previously unreported manner. With the structural information, we ascertained CfrX as a thioredoxin-like ferredoxin. While the precise function of CfrX in cobalamin biosynthesis is elusive, a link between CfrX and aerobic cobaltochelatase should exist due to the gene clustering pattern. We also discussed the possible relationship among CfrX, CobW, and CobNST with respect to the [2Fe-2S] cluster.

Cholesterol-dependent enzyme activity of human TSPO1

The amino acid sequence of the tryptophan-rich sensory proteins (TSPO) is substantially conserved throughout all kingdoms of life. Human mitochondrial TSPO1 (HsTSPO1) binds to porphyrins and steroids, although its interactions with these molecules remains unknown. HsTSPO1 is associated with numerous physiological and pathological disorders, but the underlying molecular mechanisms are unknown. Here, we disclose the finding of human mitochondrial TSPO as a cholesterol-dependent protoporphyrin IX oxygenase. The results of our biochemical characterization are consistent with structural data and evolutionary analysis. The dependence of HsTSPO1 activity on cholesterol may be the result of the coevolution of this membrane protein with the membrane system. Our study provides a molecular foundation for comprehending the various roles played by mitochondrial TSPO in normal physiological and pathological situations.

Trans-nuclease activity of Cas9 activated by DNA or RNA target binding

Type V and type VI CRISPR-Cas systems have been shown to cleave nonspecific single-stranded DNA (ssDNA) or single-stranded RNA (ssRNA) in trans, but this has not been observed in type II CRISPR-Cas systems using single guide RNA. We show here that the type II CRISPR-Cas9 systems directed by CRISPR RNA and trans-activating CRISPR RNA dual RNAs show RuvC domain-dependent trans-cleavage activity for both ssDNA and ssRNA substrates. Cas9 possesses sequence preferences for trans-cleavage substrates, preferring to cleave T- or C-rich ssDNA substrates. We find that the trans-cleavage activity of Cas9 can be activated by target ssDNA, double-stranded DNA and ssRNA. The crystal structure of Cas9 in complex with guide RNA and target RNA provides a structural basis for the binding of target RNA to activate Cas9. Based on the trans-cleavage activity of Cas9 and nucleic acid amplification technology, we develop the nucleic acid detection platforms DNA-activated Cas9 detection and RNA-activated Cas9 detection, which are capable of detecting DNA and RNA samples with high sensitivity and specificity.

Structure-Guided Engineering of a Versatile Urethanase Improves Its Polyurethane Depolymerization Activity

Polyurethane (PUR), the fifth most prevalent synthetic polymer, substantially contributes to the global plastic waste problem. Biotechnology-based recycling methods have recently emerged as innovative solutions to plastic waste disposal and sparked interest among scientific communities and industrial stakeholders in discovering and designing highly active plastic-degrading enzymes. Here, the ligand-free crystal structure of UMG-SP2, a metagenome-derived urethanase with depolymerization activities, at 2.59 Å resolution, as well as its (co-)structures bound to a suicide hydrolase inhibitor and a short-chain carbamate substrate at 2.16 and 2.40 Å resolutions, respectively, is reported. Structural analysis and molecular dynamics simulations reveal that the flexible loop L3 consisting of residues 219-226 is crucial for regulating the hydrolytic activity of UMG-SP2. The semi-rational redesign of UMG-SP2 reveals superior variants, A141G and Q399A, exhibiting over 30.7- and 7.4-fold increased activities on polyester-PUR and a methylene diamine derivative of PUR, respectively, compared to the wild-type enzyme. These findings advance the understanding of the structure-function relationship of PUR-hydrolyzing enzymes, which hold great promise for developing effective industrial PUR recycling processes and mitigating the environmental footprint of plastic waste.

Structural basis for the fast maturation of pcStar, a photoconvertible fluorescent protein

Green-to-red photoconvertible fluorescent proteins (PCFPs) serve as key players in single-molecule localization super-resolution imaging. As an early engineered variant, mEos3.2 has limited applications, mostly due to its slow maturation rate. The recent advent of a novel variant, pcStar, obtained by the simple mutation of only three amino acids (D28E/L93M/N166G) in mEos3.2, exhibits significantly accelerated maturation and enhanced fluorescent brightness. This improvement represents an important advance in the field of biofluorescence by enabling early detection with reliable signals, essential for labelling dynamic biological processes. However, the mechanism underlying the significant improvement in fluorescent performance from mEos3.2 to pcStar remains elusive, preventing the rational design of more robust variants through mutagenesis. In this study, we determined the crystal structures of mEos3.2 and pcStar in their green states at atomic resolution and performed molecular-dynamics simulations to reveal significant divergences between the two proteins. Our structural and computational analyses revealed crucial features that are distinctively present in pcStar, including the presence of an extra solvent molecule, high conformational stability and enhanced interactions of the chromophore with its surroundings, tighter tertiary-structure packing and dynamic central-helical deformation. Resulting from the triple mutations, all of these structural features are likely to establish a mechanistic link to the greatly improved fluorescent performance of pcStar. The data described here not only provide a good example illustrating how distant amino-acid substitutions can affect the structure and bioactivity of a protein, but also give rise to strategic considerations for the future engineering of more widely applicable PCFPs.

The 2-methylcitrate cycle and the glyoxylate shunt in Pseudomonas aeruginosa are linked through enzymatic redundancy

The 2-methylcitrate cycle and the glyoxylate cycle are central metabolic pathways in Pseudomonas aeruginosa, enabling the organism to utilize organic acids such as propionate and acetate during infection. Here, we show that these cycles are linked through enzymatic redundancy, with isocitrate lyase (AceA) exhibiting secondary 2-methylisocitrate lyase activity. Furthermore, we use a combination of structural analyses, enzyme kinetics, metabolomics, and targeted mutation of PrpBPa to demonstrate that whereas loss of PrpB function impairs growth on propionate, the promiscuous 2-methylisocitrate lyase activity of AceA compensates for this by mitigating the accumulation of toxic 2-methylcitrate cycle intermediates. Our findings suggest that simultaneous inhibition of PrpB and AceA could present a robust antimicrobial strategy to target P. aeruginosa in propionate-rich environments, such as the cystic fibrosis airways. Our results emphasize the importance of understanding pathway interconnections in the development of novel antimicrobial agents.

Lysine carbamoylation during urea denaturation remodels the energy landscape of human transthyretin dissociation linked to unfolding

Chemical denaturants such as urea have become indispensable in modern protein science for measuring the energetics of protein folding and assembly. Denaturants bind to and preferentially stabilize denatured states, folding transition states, and folding intermediates over the native state, allowing experimental access to free energies of folding and insights into folding mechanisms. However, too little attention is paid to the established chemical instability of aqueous urea, that is, its decomposition into the reactive electrophile ammonium cyanate or isocyanic acid depending on the solution pH. Protein carbamoylation by cyanate/isocyanic acid can change the dissociation and/or unfolding free energy landscape of the protein under study with time. This problem is exemplified using the human blood protein transthyretin (TTR), a kinetically stable transporter of thyroid hormone and holo-retinol binding protein. The dissociation, misfolding, and aggregation of TTR are associated with a prominent human amyloid disease. We demonstrate that modification of TTR by cyanate reshapes the energy landscape of TTR tetramer dissociation and unfolding on multiple time scales. Like certain halide anions and the more chemically inert thiocyanate anion, cyanate binds weakly and non-covalently to the thyroid hormone binding interface in the TTR tetramer. The close proximity of the bound cyanate ion to the pKa-perturbed lysine 15 ε-amino side chain nucleophile in the thyroid hormone binding sites of TTR favors carbamoylation of this nitrogen. Lysine 15 ε-amino carbamoylation substantially slows down TTR tetramer dissociation mediated by urea denaturation, thus introducing kinetic heterogeneity early in the unfolding reaction. Slower carbamoylation of the subpopulation of other, less pKa-perturbed lysine ε-amino groups hastens tetramer unfolding, leading to non-exponential, sigmoidal unfolding trajectories. We thus demonstrate that lysine carbamoylation in urea solutions can strongly alter protein unfolding energetics and the mechanism of unfolding.

Structure and activity of a phosphinothricin N-acetyltransferase (PSPTO_3321) from Pseudomonas syringae pv. tomato DC3000

Phosphinothricin inhibits plant glutamine synthetase and is used as a herbicide. Streptomyces hygroscopicus and Streptomyces viridochromogenes, which produce phosphinothricin naturally, encode acetyltransferases that confer phosphinothricin resistance. In the Pseudomonas genome database, a number of proteins have been annotated as phosphinothricin acetyltransferases and putative phosphinothricin acetyltransferases. One such protein is PSPTO_3321 from P. syringae, a strain that causes tomato speck. Here, we reveal that PSPTO_3321 from P. syringae, termed syr_pat, is a phosphinothricin acetyltransferase, and also retains a lower level of activity against the structurally similar substrate methionine sulfoximine. We solved a 1.6 Å resolution crystal structure of syr_pat alone and a 2.5 Å resolution structure for a complex with L-phosphinothricin. We also characterised active site mutants, providing insights into substrate specificity. Our work now provides a basis for further study of the reaction mechanism.

Albumins constrainting the conformation of mitochondria-targeted photosensitizers for tumor-specific photodynamic therapy

Tumor ablation Preclinical organelle-targeted phototherapies have effectively achieved tumor photoablation for regenerative biomedical applications in cancer therapies. However, engineering effective phototherapy drugs with precise tumor-localization targeting and organelle direction remains challenging. Herein, we report a albumins constrainting mitochondrial-targeted photosensitizer nanoparticles (PSs@BSAs) for tumor-specific photodynamic therapy. X-ray crystallography elucidates the two-stage assembly mechanism of PSs@BSAs. Femtosecond transient absorption spectroscopy and quantum mechanical calculations reveal the implications of conformational dynamics at the excited state. PSs@BSAs can efficiently disable mitochondrial activity, and further disrupt tumor angiogenesis based on the photodynamic effect. This triggers a metabolic and oxidative stress crisis to facilitate photoablation of solid tumor and antitumor metastasis. The study fully elucidates the interdisciplinary issues of chemistry, physics, and biological interfaces, thereby opening new horizons to inspire the engineering of organelle-targeted tumor-specific photosensitizers for biomedical applications.

Structural characterization of dUTPase from Legionella pneumophila

Cellular deoxyuridine 5'-triphosphate nucleotidohydrolases (dUTPases) catalyze the hydrolysis of deoxyuridine triphosphate (dUTP) to deoxyuridine monophosphate (dUMP) and pyrophosphate (PPi). dUTPase is an essential metabolic enzyme which maintains the homeostatic dTTP:dUTP ratio. As DNA polymerases are unable to distinguish between thymine and uracil during replication, the dTTP:dUTP ratio is essential for preventing the misincorporation of uracil into DNA. In the absence of dUTPase regulation of the dTTP:dUTP ratio, many DNA double-strand breaks are induced by DNA-repair enzymes, which may ultimately lead to cell death. Legionnaires' disease is a rare but severe respiratory infection caused primarily by Legionella pneumophila serogroup 1. Increased characterization of the L. pneumophila proteome is of interest for the development of new treatments. Many DNA metabolism proteins have yet to be characterized in L. pneumophila, including dUTPase. Here, we present analysis of two crystal structures of L. pneumophila dUTPase in its apo and dUMP-bound states, determined to 1.80 and 1.95 Å resolution, respectively. The structures were solved by the Seattle Structural Genomics Center for Infectious Disease (SSGCID) as part of their mission to determine structures of proteins and other molecules with an important biological role in human pathogens.

De novo discovery of a molecular glue-like macrocyclic peptide that induces MCL1 homodimerization

Macrocyclic peptides have emerged as promising drug candidates, filling the gap between small molecules and large biomolecules in drug discovery. The antiapoptotic protein myeloid cell leukemia 1 (MCL1) is crucial for numerous cancers, yet it presents challenges for selective targeting by traditional inhibitors. In this study, we identified a macrocyclic peptide, 5L1, that strongly binds to MCL1, with a dissociation constant (KD) of 7.1 nM. This peptide shows the potential to specifically inhibit the function of MCL1, and demonstrates effective antitumor activity against several blood tumor cell lines with the half maximal inhibitory concentration (IC50) values for cell-penetrating peptide-conjugated 5L1 in the range of 0.6 to 3 μM. Structural analysis revealed that it functions similarly to molecular glue, capable of binding to two MCL1 molecules simultaneously and inducing their homodimerization. This unique mechanism of action distinguishes it from traditional small-molecule MCL1 inhibitors, underscoring the potential of macrocyclic peptides functioning as molecular glues. Moreover, it inspires the development of highly selective inhibitors targeting MCL1 and other related targets with this glue-like mechanism.

A generic cross-seeding approach to protein crystallization

Obtaining diffraction-quality crystals is often the rate-limiting step during structure determination of biological macromolecules by X-ray crystallography. To address this problem, we investigated a cross-seeding approach with a mixture integrating a heterogeneous set of protein crystal fragments to be used as generic seeds. The fragments are nanometre-sized templates chosen to promote crystal nucleation of protein samples unrelated to the proteins forming the seeds. An atypical crystal form of the human serine hydrolase retinoblastoma binding protein 9 was obtained by adding the mixture to the protein sample before performing standard crystallization assays. The structure was solved by X-ray crystallography at 1.4 Å resolution. Follow-up experiments showed that crystal fragments of α-amylase were critical components in this particular result. The limitations and future applications of our experimental developments are discussed.

A miniature CRISPR-Cas10 enzyme confers immunity by an inverse signaling pathway

Microbial and viral co-evolution has created immunity mechanisms involving oligonucleotide signaling that share mechanistic features with human anti-viral systems 1 . In these pathways, including CBASS and type III CRISPR systems in bacteria and cGAS-STING in humans, oligonucleotide synthesis occurs upon detection of virus or foreign genetic material in the cell, triggering the antiviral response 2-4 . In a surprising inversion of this process, we show here that the CRISPR-related enzyme mCpol synthesizes cyclic oligonucleotides constitutively as part of an active mechanism that maintains cell health. Cell-based experiments demonstrated that the absence or loss of mCpol-produced cyclic oligonucleotides triggers cell death, preventing spread of viruses that attempt immune evasion by depleting host cyclic nucleotides. Structural and mechanistic investigation revealed mCpol to be a di-adenylate cyclase whose product, c-di-AMP, prevents toxic oligomerization of the effector protein 2TMβ. Analysis of cells by fluorescence microscopy showed that lack of mCpol allows 2TMβ-mediated cell death due to inner membrane collapse. These findings unveil a powerful new defense strategy against virus-mediated immune suppression, expanding our understanding of oligonucleotides in cell health and disease. These results raise the possibility of similar protective roles for cyclic oligonucleotides in other organisms including humans.

Crystal structure of ferric recombinant horseradish peroxidase

Horseradish peroxidase (HRP), isolated from horseradish roots, is heavily glycosylated, making it difficult to crystallize. In this work, we produced recombinant HRP in E. coli and obtained an X-ray structure of the ferric enzyme at 1.63 Å resolution. The structure shows that the recombinant HRP contains four disulphide bonds and two calcium ions, which are highly conserved in class III peroxidase enzymes. The heme active site contains histidine residues at the proximal (His 170) and distal (His 42) positions, and an active site arginine (Arg 38). Surprisingly, an ethylene glycol molecule was identified in the active site, forming hydrogen bonds with His 42 and Arg 38 at the δ-heme edge. The high yields obtained from the recombinant expression system, and the successful crystallization of the enzyme pave the way for new structural studies in the future.

Functional and structural characterization of Staphylococcus aureus N-acetylglucosamine 1-phosphate uridyltransferase (GlmU) reveals a redox-sensitive acetyltransferase activity

The bifunctional enzyme N-acetylglucosamine 1-phosphate uridyltransferase (GlmU) is a promising antibiotic drug target, as it facilitates the biosynthesis of uridine 5'-diphospho-N-acetylglucosamine, an essential precursor of cell wall constituents. We identified that Staphylococcus aureus GlmU (SaGlmU), which was previously targeted for inhibitor development, possesses a dual-cysteine variation (C379/C404) within the acetyltransferase active site. Enzyme assays performed under reducing and non-reducing conditions revealed that the acetyltransferase activity of SaGlmU is redox-sensitive, displaying ~15-fold lower turnover and ~3-fold higher KM value for the acetyl CoA substrate under non-reducing conditions. This sensitivity was absent in a C379A SaGlmU mutant. Analysis of SaGlmU by mass spectrometry, x-ray crystallography, and in silico modeling support that C379 and C404 act as a reversible, redox-sensitive switch by forming a disulfide under non-reducing conditions that impedes acetyl CoA recognition and turnover. Therefore, we recommend that future in vitro screening and characterization of SaGlmU inhibitors consider both reducing and non-reducing conditions.

Cancer hotspot mutations rewire ERK2 specificity by selective exclusion of docking interactions

The protein kinase ERK2 is recurrently mutated in human squamous cell carcinomas and other tumors. ERK2 mutations cluster in an essential docking recruitment site that interacts with short linear motifs found within intrinsically disordered regions of ERK substrates and regulators. Cancer-associated mutations do not disrupt ERK2 docking interactions altogether but selectively inhibit some interactions while sparing others. However, the full scope of disrupted or maintained interactions remains unknown, limiting our understanding of how these mutations contribute to cancer. We recently defined the docking interactome of wild-type ERK2 by screening a yeast two-hybrid library of proteomic short linear motifs. Here, we apply this approach to the two most recurrent cancer-associated mutants. We find that most sequences binding to WT ERK2 also interact with both mutant forms. Analysis of differentially interacting sequences revealed that ERK2 mutants selectively lose the ability to bind sequences conforming to a specific motif. We solved the co-crystal structure of ERK2 in complex with a peptide fragment of ISG20, a screening hit that binds exclusively to the WT kinase. This structure demonstrated the mechanism by which cancer hotspot mutations at Glu81, Arg135, Asp321, and Glu322 selectively impact peptide binding. Finally, we found that cancer-associated ERK2 mutations had decreased activity in phosphorylating GEF-H1/ARHGEF2, a known ERK substrate harboring a WT-selective docking motif. Collectively, our studies provide a structural rationale for how a broad set of interactions are disrupted by ERK2 hotspot mutations, suggesting mechanisms for pathway rewiring in cancers harboring these mutations.

Capture, mutual inhibition and release mechanism for aPKC-Par6 and its multisite polarity substrate Lgl

The mutually antagonistic relationship of atypical protein kinase C (aPKC) and partitioning-defective protein 6 (Par6) with the substrate lethal (2) giant larvae (Lgl) is essential for regulating polarity across many cell types. Although aPKC-Par6 phosphorylates Lgl at three serine sites to exclude it from the apical domain, aPKC-Par6 and Lgl paradoxically form a stable kinase-substrate complex, with conflicting roles proposed for Par6. We report the structure of human aPKCι-Par6α bound to full-length Llgl1, captured through an aPKCι docking site and a Par6PDZ contact. This complex traps a phospho-S663 Llgl1 intermediate bridging between aPKC and Par6, impeding phosphorylation progression. Thus, aPKCι is effectively inhibited by Llgl1pS663 while Llgl1 is captured by aPKCι-Par6. Mutational disruption of the Lgl-aPKC interaction impedes complex assembly and Lgl phosphorylation, whereas disrupting the Lgl-Par6PDZ contact promotes complex dissociation and Lgl phosphorylation. We demonstrate a Par6PDZ-regulated substrate capture-and-release model requiring binding by active Cdc42 and the apical partner Crumbs to drive complex disassembly. Our results suggest a mechanism for mutual regulation and spatial control of aPKC-Par6 and Lgl activities.

The Crystal Structure of Human IgD-Fc Reveals Unexpected Differences With Other Antibody Isotypes

Of the five human antibody isotypes, the function of IgD is the least well-understood, although various studies point to a role for IgD in mucosal immunity. IgD is also the least well structurally characterized isotype. Until recently, when crystal structures were reported for the IgD Fab, the only structural information available was a model for intact IgD based on solution scattering data. We now report the crystal structure of human IgD-Fc solved at 3.0 Å resolution. Although similar in overall architecture to other human isotypes, IgD-Fc displays markedly different orientations of the Cδ3 domains in the Cδ3 domain dimer and the lowest interface area of all the human isotypes. The nature of the residues that form the dimer interface also differs from those conserved in the other isotypes. By contrast, the interface between the Cδ2 and Cδ3 domains in each chain is the largest among the human isotypes. This interface is characterized by two binding pockets, not seen in other isotypes, and points to a potential role for the Cδ2/Cδ3 interface in stabilizing the IgD-Fc homodimer. We investigated the thermal stability of IgD-Fc, alone and in the context of an intact IgD antibody, and found that IgD-Fc unfolds in a single transition. Human IgD-Fc clearly has unique structural features not seen in the other human isotypes, and comparison with other mammalian IgD sequences suggests that these unique features might be widely conserved.

Characterization of Arabidopsis thaliana FRATAXIN HOMOLOG in heme catabolism

Frataxin plays vital roles in various iron related processes. Arabidopsis thaliana FRATAXIN HOMOLOG (AtFH) is the first identified plant frataxin and has been found to regulate the last step of heme biosynthesis. Here, we report the involvement of AtFH in heme catabolism by regulating the activity of heme oxygenase. AtFH forms a homodimer, and its crystal structure shows the dimeric interactions. A structural comparison with known frataxin structures suggests the iron binding sites, and the site for heme oxygenase activity is possibly located in a region containing Glu78. The results indicate a previously uncharacterized role of plant frataxin in heme catabolism.

A broad-spectrum lasso peptide antibiotic targeting the bacterial ribosome

Lasso peptides (biologically active molecules with a distinct structurally constrained knotted fold) are natural products that belong to the class of ribosomally synthesized and post-translationally modified peptides1-3. Lasso peptides act on several bacterial targets4,5, but none have been reported to inhibit the ribosome, one of the main targets of antibiotics in the bacterial cell6,7. Here we report the identification and characterization of the lasso peptide antibiotic lariocidin and its internally cyclized derivative lariocidin B, produced by Paenibacillus sp. M2, which has broad-spectrum activity against a range of bacterial pathogens. We show that lariocidins inhibit bacterial growth by binding to the ribosome and interfering with protein synthesis. Structural, genetic and biochemical data show that lariocidins bind at a unique site in the small ribosomal subunit, where they interact with the 16S ribosomal RNA and aminoacyl-tRNA, inhibiting translocation and inducing miscoding. Lariocidin is unaffected by common resistance mechanisms, has a low propensity for generating spontaneous resistance, shows no toxicity to human cells, and has potent in vivo activity in a mouse model of Acinetobacter baumannii infection. Our identification of ribosome-targeting lasso peptides uncovers new routes towards the discovery of alternative protein-synthesis inhibitors and offers a novel chemical scaffold for the development of much-needed antibacterial drugs.

Structures of Legionella pneumophila serogroup 1 peptide deformylase bound to nickel(II) and actinonin

Legionella pneumophila serogroup 1 is the primary causative agent of Legionnaires' disease, a rare but severe respiratory infection. While the fatality rate of Legionnaires' disease is low in the general population, it is more pronounced in vulnerable communities such as the immunocompromised. Thus, the development of new antimicrobials is of interest for use when existing antibiotics may not be applicable. Peptide deformylases (PDFs) have been under continued investigation as targets for novel antimicrobial compounds. PDF plays an essential role in protein synthesis, removing the N-terminal formyl group from new polypeptides, and is required for growth in most bacteria. Here, we report two crystal structures of L. pneumophila serogroup 1 PDF (LpPDF) bound to either Ni2+, an active state, or inhibited by actinonin and Zn2+; the structures were determined to 1.5 and 1.65 Å resolution, respectively, and were solved by the Seattle Structural Genomics Center for Infectious Disease (SSGCID). The SSGCID is charged with determining structures of biologically important proteins and molecules from human pathogens. As actinonin is an antimicrobial natural product that has been used as a reference compound in drug development, these structures will help support the ongoing drug-development process.

The High-Resolution Structure of a Variable Lymphocyte Receptor From Petromyzon marinus Capable of Binding to the Brain Extracellular Matrix

Variable lymphocyte receptors (VLRs) are antigen receptors derived from the adaptive immune system of jawless vertebrates such as lamprey ( Petromyzon marinus ). First discovered in 2004, VLRs have been the subject of numerous biochemical and structural investigations. Due to their unique antigen binding properties, VLRs have been leveraged as possible drug delivery agents. One such VLR, previously identified and referred to as P1C10, was shown to bind to the brain extracellular matrix. Here, we present the high-resolution X-ray crystal structure of this VLR determined to 1.3 Å resolution. The fold is dominated by a six-stranded mixed β-sheet which provides a concave surface for possible antigen binding. Electron density corresponding to a 4-(2-hydroxyethyl)piperazine-1-propanesulfonic acid buffer molecule (HEPPS) was found in this region. By comparing the P1C10 molecular architecture and its buffer binding residues with those of other VLRs previously reported, it was possible to illustrate how this unique class of proteins can accommodate diverse binding partners. Additionally, we provide an analysis of the experimentally determined structure compared to the models generated by the commonly used AlphaFold and iTASSER structure prediction software packages.

Selective G6PDH inactivation for Helicobacter pylori eradication with transformed polysulfide

Alternative treatment for the highly prevalent Helicobacter pylori infection is imperative due to rising antibiotic resistance. We unexpectedly discovered that the anti-H. pylori component in garlic is hydrogen polysulfide (H2Sn, n⩾2), not organic polysulfides. Studies on the mechanism of action (MoA) show that H2Sn specifically inactivates H. pylori glucose-6-phosphate dehydrogenase (G6PDH) by interfering with electron transfer from glucose-6-phosphate (G6P) to nicotinamide adenine dinucleotide phosphate (NADP+). However, low H2Sn yield makes garlic derivatives hard to be a reliable donor of H2Sn to treat H. pylori infection. To address this challenge, we established a polysulfide transformation process from garlic organosulfur compounds into Fe3S4 that generates H2Sn with a 25-58 times increase in yield. Through chitosan encapsulation, we designed a gastric-adaptive H2Sn microreactor (GAPSR) that eradicates H. pylori with 250 times higher efficiency under gastric conditions. A single GAPSR achieves more rapid H. pylori eradication than combined antibiotics therapy without disturbing the gut microbiota. These findings indicate a distinct MoA transformation mediated by polysulfide as an alternative candidate to treat H. pylori infection.

Discovery of a fluorinated macrobicyclic antibiotic through chemical synthesis

The emergence of bacterial antimicrobial resistance threatens to undermine the utility of antibiotic therapy in medicine. This threat can be addressed, in part, by reinventing existing antibiotic classes using chemical synthesis. Here we present the discovery of BT-33, a fluorinated macrobicyclic oxepanoprolinamide antibiotic with broad-spectrum activity against multidrug-resistant bacterial pathogens. Structure-activity relationships within the macrobicyclic substructure reveal structural features that are essential to the enhanced potency of BT-33 as well as its increased metabolic stability relative to its predecessors clindamycin, iboxamycin and cresomycin. Using X-ray crystallography, we determine the structure of BT-33 in complex with the bacterial ribosome revealing that its fluorine atom makes an additional van der Waals contact with nucleobase G2505. Through variable-temperature 1H NMR experiments, density functional theory calculations and vibrational circular dichroism spectroscopy, we compare macrobicyclic homologues of BT-33 and a C7 desmethyl analogue and find that the C7 methyl group of BT-33 rigidifies the macrocyclic ring in a conformation that is highly preorganized for ribosomal binding.

Phylogenetic analysis and structural studies of heteromeric acetyl-CoA carboxylase from the oleaginous Amazonian microalgae Ankistrodesmus sp.: Insights into the BC and BCCP subunits

Acetyl-CoA carboxylase (ACC) is an essential enzyme in fatty acid biosynthesis that catalyzes the formation of malonyl-CoA from acetyl-CoA. While structural studies on ACC components have largely focused on prokaryotes and higher plants, the assembly and molecular adaptations of ACC in microalgae remain underexplored. This study aimed to fill this gap by providing the first structural and evolutionary characterization of both biotin carboxylase (BC) and biotin carboxyl carrier protein (BCCP) from a microalga (Ankistrodesmus sp.). Phylogenetic analysis revealed distinct evolutionary trajectories for BC and BCCP, with BC forming a chlorophyte-specific clade closely related to other oleaginous species, while BCCP displayed two distinct isoforms within green algae, resulting from gene duplication. The crystallographic structure of BC was solved in its apo (1.75 Å) and ADP-Mg2+-bound (1.90 Å) states, revealing conserved conformational changes associated with cofactor binding. BCCP from Ankistrodesmus sp. displayed a unique QLGTF/H motif instead of the canonical AMKXM biotinylation motif, suggesting loss of biotinylation capacity. However, the presence of three additional lysines in the protruding thumb loop, with Lys95 as a candidate for biotin attachment, indicates potential compensatory adaptations. SEC-MALS and pull-down assays confirmed the formation of a stable 1:1 BC-BCCP complex, and circular dichroism showed increased thermal stability of the complex, supporting its structural stability. This study highlights unique structural adaptations in Ankistrodesmus sp. ACC, emphasizing the evolutionary plasticity of BC and BCCP. These insights provide a foundation for future investigations into ACC regulation in photosynthetic organisms and offer potential biotechnological applications for optimizing lipid production in microalgae.

Allosteric inhibition of trypanosomatid pyruvate kinases by a camelid single-domain antibody

African trypanosomes are the causative agents of neglected tropical diseases affecting both humans and livestock. Disease control is highly challenging due to an increasing number of drug treatment failures. African trypanosomes are extracellular, blood-borne parasites that mainly rely on glycolysis for their energy metabolism within the mammalian host. Trypanosomal glycolytic enzymes are therefore of interest for the development of trypanocidal drugs. Here, we report the serendipitous discovery of a camelid single-domain antibody (sdAb aka Nanobody) that selectively inhibits the enzymatic activity of trypanosomatid (but not host) pyruvate kinases through an allosteric mechanism. By combining enzyme kinetics, biophysics, structural biology, and transgenic parasite survival assays, we provide a proof-of-principle that the sdAb-mediated enzyme inhibition negatively impacts parasite fitness and growth.

Glutamate indicators with increased sensitivity and tailored deactivation rates

Identifying the input-output operations of neurons requires measurements of synaptic transmission simultaneously at many of a neuron's thousands of inputs in the intact brain. To facilitate this goal, we engineered and screened 3365 variants of the fluorescent protein glutamate indicator iGluSnFR3 in neuron culture, and selected variants in the mouse visual cortex. Two variants have high sensitivity, fast activation (< 2 ms) and deactivation times tailored for recording large populations of synapses (iGluSnFR4s, 153 ms) or rapid dynamics (iGluSnFR4f, 26 ms). By imaging action-potential evoked signals on axons and visually-evoked signals on dendritic spines, we show that iGluSnFR4s/4f primarily detect local synaptic glutamate with single-vesicle sensitivity. The indicators detect a wide range of naturalistic synaptic transmission, including in the vibrissal cortex layer 4 and in hippocampal CA1 dendrites. iGluSnFR4 increases the sensitivity and scale (4s) or speed (4f) of tracking information flow in neural networks in vivo.

Isoleucine binding and regulation of Escherichia coli and Staphylococcus aureus threonine dehydratase (IlvA)

In Staphylococcus aureus, the branched-chain amino acid biosynthetic pathway provides essential intermediates for membrane biosynthesis. Threonine deaminase (IlvA) is the first enzyme in the pathway, and isoleucine feedback-regulates the enzyme in Escherichia coli. These studies on E. coli IlvA (EcIlvA) introduced the concept of allosteric regulation. To investigate the regulation of S. aureus IlvA (SaIlvA), we first conducted additional studies on EcIlvA. The previously determined crystal structure of EcIlvA revealed a tetrameric assembly of protomers, each with catalytic and regulatory domains, but the structural basis of isoleucine regulation was not characterized. Here, we present the crystal structure of the EcIlvA regulatory domain bound to isoleucine, which reveals the isoleucine binding site and conformational changes that initiate at Phe352 and propagate 23 Angstrom across the domain. This suggests an allosteric pathway that extends to the active site of the adjacent protomer, mediating regulation across the protomer-protomer interface. The EcIlvA(F352A) mutant binds isoleucine but is feedback-resistant due to the absence of the initiating Phe352. In contrast, SaIlvA is not feedback-regulated by isoleucine and does not bind it. The structure of the SaIlvA regulatory domain reveals a different organization that lacks the isoleucine binding site. Other potential allosteric inhibitors of SaIlvA, including phospholipid intermediates, do not affect enzyme activity. We propose that the absence of feedback inhibition in SaIlvA is due to its role in membrane biosynthesis. These findings enhance our understanding of IlvA's allosteric regulation and offer opportunities for engineering feedback-resistant IlvA variants for biotechnological use.

Controlling outer-sphere solvent reorganization energy to turn on or off the function of artificial metalloenzymes

Metalloenzymes play essential roles in biology. However, unraveling how outer-sphere interactions can be predictably controlled to influence their functions remains a significant challenge. Inspired by Cu enzymes, we demonstrate how variations in the primary, secondary, and outer coordination-sphere interactions of de novo designed artificial copper proteins (ArCuPs) within trimeric (3SCC) and tetrameric (4SCC) self-assemblies-featuring a trigonal Cu(His)3 and a square pyramidal Cu(His)4(OH2) coordination-influence their catalytic and electron transfer properties. While 3SCC electrocatalyzes C-H oxidation, 4SCC does not. CuI-3SCC reacts more rapidly with H2O2 than O2, whereas 4SCC is less active. Electron transfer, reorganization energies, and extended H2O-mediated hydrogen bonding patterns provide insights into the observed reactivity differences. The inactivity of 4SCC is attributed to a significant solvent reorganization energy barrier mediated by a specific His---Glu hydrogen bond. When this hydrogen bond is disrupted, the solvent reorganization energy is reduced, and C-H peroxidation activity is restored.

Structure of the lens MP20 mediated adhesive junction

Human lens fiber membrane intrinsic protein MP20 is the second most abundant membrane protein of the human eye lens. Despite decades of effort its structure and function remained elusive. Here, we determined the MicroED structure of full-length human MP20 in lipidic-cubic phase to a resolution of 3.5 Å. MP20 forms tetramers each of which contain 4 transmembrane α-helices that are packed against one another forming a helical bundle. We find that each MP20 tetramer formed adhesive interactions with an opposing tetramer in a head-to-head fashion. Investigation of MP20 localization in human lenses indicate that in young fiber cells MP20 is initially localized to the cytoplasm in differentiating fiber cells but upon fiber cell maturation is inserted into the plasma membrane, correlating with the restriction of the diffusion of extracellular tracers into the lens. Together these results suggest that MP20 forms lens thin junctions in vivo, confirming its role as a structural protein in the human eye lens essential for its optical transparency.

Molecular basis underpinning MR1 allomorph recognition by an MR1-restricted T cell receptor

Introduction

The MHC-class-I-related molecule MR1 presents small metabolites of microbial and self-origin to T cells bearing semi-invariant or variant T cell receptors. One such T cell receptor, MC.7.G5, was previously shown to confer broad MR1-restricted reactivity to tumor cells but not normal cells, sparking interest in the development of non-MHC-restricted immunotherapy approaches.

Methods/Results

Here we provide cellular, biophysical, and crystallographic evidence that the MC.7.G5 TCR does not have pan-cancer specificity but is restricted to a rare allomorph of MR1, bearing the R9H mutation.

Discussion

Our results underscore the importance of in-depth characterization of MR1-reactive TCRs against targets expressing the full repertoire of MR1 allomorphs.

Determining T-cell receptor binding orientation and Peptide-HLA interactions using cross-linking mass spectrometry

T cell receptors (TCRs) recognize specific peptides presented by human leukocyte antigens (HLAs) on the surface of antigen-presenting cells and are involved in fighting pathogens and cancer surveillance. Canonical docking orientation of TCRs to their target peptide-HLAs (pHLAs) is essential for T cell activation, with reverse binding TCRs lacking functionality. TCR binding geometry and molecular interaction footprint with pHLAs are typically obtained by determining the crystal structure. Here, we describe the use of a cross-linking tandem mass spectrometry (XL-MS/MS) method to decipher the binding orientation of several TCRs to their target pHLAs. Cross-linking sites were localized to specific residues and their molecular interactions showed differentiation between TCRs binding in canonical or reverse orientations. Structural prediction and crystal structure determination of two TCR-pHLA complexes validated these findings. The XL-MS/MS method described herein offers a faster and simpler approach for elucidating TCR-pHLA binding orientation and interactions.