NE-CAT News

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...

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...

Protein kinase C (PKC) isozymes are ubiquitous kinases that direct diverse cellular pathways and are important drug targets for the treatment of cancer and neurological diseases. PKCs are auto-regulating enzymes governed by phospholipid and Ca^(2+) signals via a mechanism that has remained enigmatic due to a paucity of structural information. Herein we present a series of structures of the full-length human PKCβI and PKCβII isozymes. These structures reveal the molecular basis by which PKCs...

Restoring the tumor suppressive activity of the Hippo signaling pathway lost through dysregulation of the NUAK1/2 and MARK2/3 kinase axis and downstream transcriptional effectors YAP/TAZ has emerged as a new modality for the treatment of several human cancers. Small molecule inhibition of NUAK1/2 and MARK2/3 constitutes a rational approach to block YAP/TAZ nuclear translocation and prevent a pro-oncogenic gene expression program. Modest structural changes to lead compound OICR14489, discovered...

Aspartate transcarbamoylase (ATCase) from Escherichia coli catalyzes a key step in pyrimidine nucleotide biosynthesis and has long served as a model for allosteric regulation. Despite decades of study, how nucleotide binding at distant regulatory sites controls cooperativity between active sites remained unresolved. Here we show that ATCase does not simply interconvert between two conformations, as traditionally depicted, but instead samples a continuum of conformations that tune enzyme...

Cellular metabolites have emerged as noncanonical RNA caps. Despite its early discovery as an RNA cap, the dephospho-CoA (dpCoA) cap remains largely uncharacterized because of a lack of detection technologies. Here we use biochemical and structural analysis to identify Arabidopsis NUDT11 as a specific decapping enzyme toward dpCoA-RNA. Leveraging this specificity, we develop biochemical and transcriptomic methods to quantify and profile dpCoA-RNA across the genome, revealing that dpCoA-RNAs...