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This paper explores the structural continuum in CATH and the extent to which superfamilies adopt distinct folds. Although most superfamilies are structurally conserved, in some of the most highly populated superfamilies (4% of all superfamilies) there is considerable structural divergence. While relatives share a similar fold in the evolutionary conserved core, diverse elaborations to this core can...
Sondermann and colleagues have characterized FimX, a protein with degenerate GGDEF and EAL domains. The study confirms the expected domain folds lacking conserved catalytic residues for c-di-GMP synthesis/degradation, and also defines domain arrangements, providing insight to regulatory mechanisms.
Although allostery draws increasing attention, not much is known about allosteric mechanisms. Here we argue that in all proteins, allosteric signals transmit through multiple, pre-existing pathways; which pathways dominate depend on protein topologies, specific binding events, covalent modifications, and cellular (environmental) conditions. Further, perturbation events at any site on the protein surface...
Cadherin homodimerization mediates cell-cell adhesion, but one stabilizing structural element has inspired questions about assembly mechanisms. Combining single molecule fluorescence and force analyses allowed Sivasankar et al. to provide strong evidence for an induced fit pathway to dimerization.
The fungal type I fatty acid synthase (FAS) is a 2.6 MDa multienzyme complex, catalyzing all necessary steps for the synthesis of long acyl chains. To be catalytically competent, the FAS must be activated by a posttranslational modification of the central acyl carrier domain (ACP) by an intrinsic phosphopantetheine transferase (PPT). However, recent X-ray structures of the fungal FAS revealed a barrel-shaped...
We compared the modes of interaction between protein-peptide interfaces and those observed within monomeric proteins and found surprisingly few differences. Over 65% of 731 protein-peptide interfaces could be reconstructed within 1 Å RMSD using solely fragment interactions occurring in monomeric proteins. Interestingly, more than 80% of interacting fragments used in reconstructing a protein-peptide...
Cadherins are Ca 2+ -dependent cell-cell adhesion proteins with an extracellular region of five domains (EC1 to EC5). Adhesion is mediated by “strand swapping” of a conserved tryptophan residue in position 2 between EC1 domains of opposing cadherins, but the formation of this structure is not well understood. Using single-molecule fluorescence resonance energy transfer and single-molecule...
SH2 domains are phosphotyrosine specific interaction modules with largely overlapping sequence specificities. A recent structure by Bae et al. revealed that SH2 domain specificity can be mediated by secondary binding sites located outside the phosphotyrosine binding pocket.
A prominent surface loop links the first two β strands of the lipoyl domain (E2plip) from the pyruvate dehydrogenase multienzyme complex of Escherichia coli. We show here that shortening this loop by two residues generates a protein that populates two structurally distinct stable conformers: an active, native-like monomer (HM) and a functionally compromised misfolded dimer (LM). Conversion of LM to...
We identify a structural feature of transmembrane helical proteins that restricts their conformational space and suggests a new way of understanding the construction and stability of their native states. We show that five kinds of well-known specific favorable interhelical interactions (hydrogen bonds, aromatic interactions, salt bridges, and two interactions from packing motifs) precisely determine...
Nucleocytoplasmic transport is mediated by nuclear pore complexes (NPCs), enormous protein assemblies residing in circular openings in the nuclear envelope. The NPC is modular, with transient and stable components. The stable core is essentially built from two multiprotein complexes, the Y-shaped heptameric Nup84 complex and the Nic96 complex, arranged around an eightfold axis. We present the crystal...
Bacterial pathogenesis involves social behavior including biofilm formation and swarming, processes that are regulated by the bacterially unique second messenger cyclic di-GMP (c-di-GMP). Diguanylate cyclases containing GGDEF and phosphodiesterases containing EAL domains have been identified as the enzymes controlling cellular c-di-GMP levels, yet less is known regarding signal transmission and the...
In this issue of Structure, Schwartz and coworkers present the structure of Nup120, a nucleoporin of the nuclear pore scaffold. The structure shows that, in contrast to earlier predictions, the nucleoporins have a larger fold repertoire than expected.
Intrinsic conformational transitions contribute to the catalytic action of many enzymes. Here we use a single-molecule approach to demonstrate how such transitions are linked to the catalytic sites of the eukaryotic proteasome, an essential protease of the ubiquitin pathway. The active sites of the cylindrical proteasomal core particle are located in a central chamber accessible through gated entry...
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