NE-CAT News

Human intrinsic factor (IF) mediates the intestinal uptake of cobalamin (Cbl; vitamin B(12)). A previous crystal structure of the IF-cobalamin complex revealed the apparent absence of an upper axial ligand at the cobalt center, raising questions regarding radiation-induced cleavage or chemical modification during crystallization. Here, high-resolution single-crystal X-ray crystallography of cobalamin in three states, oxidized and two independently prepared chemically reduced crystals, resolves...

Irreversible covalent inhibitors have garnered significant attention in recent years. Despite encouraging progress, the vast majority contain electrophiles that target the least abundant amino acid, cysteine, substantially limiting target inhibitor design for therapeutic intervention. Here, we generalize 2-ethynylbenzaldehyde as a proximity-induced electrophile for generating irreversible covalent peptide and protein inhibitors that specifically target native lysine residues. Leveraging this...

Escherichia coli topoisomerase III (EcTopo3) is a type IA topoisomerase that binds single-stranded DNA (ssDNA) during DNA cleavage and strand passage. Here, we report five crystal structures of EcTopo3 in complex with distinct 8-base ssDNA oligonucleotides at 1.85-2.22 Å resolution. These structures reveal a previously unrecognized half-open ssDNA-binding mode. In this mode, EcTopo3 engages only the five 3'-terminal nucleotides of the oligonucleotide within the conserved D4/D1 DNA-binding...

Transferrin binding protein B (TbpB), an iron acquisition protein, has long been recognized as a promising vaccine candidate targeting the pathogenic Neisseria species, including Neisseria meningitidis, the cause of meningococcal disease, and Neisseria gonorrhoeae, the cause of gonorrhea. A challenge to the development of this protein as a vaccine immunogen is the extent of antigenic variability it exhibits, which complicates the selection of a single variant to elicit a broadly cross-protective...

Cellulosomes are large, surface-displayed enzyme complexes that enable anaerobic bacteria to degrade recalcitrant plant polysaccharides, yet cellulosome-expressing bacteria are thought to be rare in the human gut. Here, we show that extensive sequence divergence obscures the detection of many ruminococcal cellulosomes by conventional sequence homology-based methods. Using proteome-scale AlphaFold2 structural predictions, we uncovered a substantially expanded set of putative cellulosome-producing...

Nervous system assembly is guided by the actions of cell surface receptors. In Drosophila, members of the beaten path (Beat) and sidestep (Side) protein families have been described as axon guidance receptor-cue pairs, in addition to roles in specifying synaptic connectivity in the optic lobe. To understand the molecular basis and specificity of Beat-Side interactions, we report here the structure of a Beat-Side complex, Beat-Vc bound to Side-VI. The structure shows a binding topology similar to...

Animal and bacterial cells defend against viral infection by rapidly activating antiviral restriction factors. In human cells, antiviral immunity is initiated by interferon signaling that results in expression of hundreds of interferon-stimulated genes (ISGs)^(1,2,3,4,5,6). Complex regulatory networks and co-evolution of viral evasion strategies complicate analysis of immune proteins under native conditions and the function of most individual ISGs remains unknown^(7,8,9,10,11,12). Here we...

Protein nanopores are powerful tools for molecular sensing, sequencing, and separation, but designing pores with programmable function remains challenging. Native homo-oligomeric transmembrane β barrels (TMBs) are used for these applications, but their uniform lumens limit spatial resolution and analyte discrimination. Although monomeric TMBs can be designed using energy-based methods, these approaches remain highly manual and limited to structural design rather than function. Here, we present a...

Bacteria encode numerous stress-response pathways that protect their hosts against both internal and external threats. A key question is how these pathways are regulated, especially anti-phage immune pathways that mediate host-cell killing. Here, we identify two proteins termed CapK and CapS that are encoded upstream of diverse immune operons, and regulate these operons' expression in response to DNA damage. CapK resembles bacterial anti-sigma factor kinases, and CapS resembles STAS-domain...

Bacterial, plant, and animal cells synthesize nucleotide immune signals as a conserved strategy to defend against viral infection^(1-4). In bacteria, Thoeris anti-phage defense systems convert nicotinamide adenine dinucleotide (NAD^(+)) into the cyclic ADP-ribose signals 2'cADPR and 3'cADPR to activate downstream effectors and restrict viral replication^(5-8). Phage proteins can bind and sequester Thoeris signals^(6,9-13), but no mechanisms are known to degrade the exceptionally stable 2'cADPR...