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Modular polyketide synthases (PKS) make novel natural products through a series of preprogrammed chemical steps catalyzed by an assembly line of multidomain modules. Each assembly-line step involves unique extension and modification reactions, resulting in tremendous diversity of polyketide products. Dehydratase domains catalyze formation of an α,β-double bond in the nascent polyketide intermediate...
Transmission electron microscopy of thin sections is the primary means for visualizing structures within cells. In this issue of Structure, Peng et al. extend this approach by using electron tomography to examine the life cycle of a herpesvirus and provide fresh insights into the processes of DNA packaging and release.
APOBEC3G is a DNA cytidine deaminase that has antiviral activity against HIV-1 and other pathogenic viruses. In this study the crystal structure of the catalytically active C-terminal domain was determined to 2.25 Å. This structure corroborates features previously observed in nuclear magnetic resonance (NMR) studies, a bulge in the second β strand and a lengthening of the second α helix. Oligomerization...
Gammaherpesviruses are etiologically associated with human tumors. A three-dimensional (3D) examination of their life cycle in the host is lacking, significantly limiting our understanding of the structural and molecular basis of virus-host interactions. Here, we report the first 3D visualization of key stages of the murine gammaherpesvirus 68 life cycle in NIH 3T3 cells, including viral attachment,...
In this issue of Structure, Golosov et al. present molecular dynamics simulations that illuminate the process of DNA translocation by an A-family DNA polymerase. Several distinct phases are identified that have not been visualized through crystallographic studies.
The opportunistic pathogen Burkholderia cenocepacia expresses several soluble lectins, among them BC2L-C. This lectin exhibits two domains: a C-terminal domain with high sequence similarity to the recently described calcium-dependent mannose-binding lectin BC2L-A, and an N-terminal domain of 156 amino acids without similarity to any known protein. The recombinant N-terminal BC2L-C domain is a new...
High-fidelity DNA polymerases copy DNA rapidly and accurately by adding correct deoxynucleotide triphosphates to a growing primer strand of DNA. Following nucleotide incorporation, a series of conformational changes translocate the DNA substrate by one base pair step, readying the polymerase for the next round of incorporation. Molecular dynamics simulations indicate that the translocation consists...
We report on the solution structure of an unprecedented intramolecular G-quadruplex formed by the guanosine-rich human chl1 intronic d(G 3 -N-G 4 -N 2 -G 4 -N-G 3 -N) 19-mer sequence in K + -containing solution. This G-quadruplex, composed of three stacked G-tetrads containing four syn guanines, represents a new folding topology with two unique conformational...
Many Gram-positive bacteria have pili attached to their cell walls, but they are much simpler and shorter than their more familiar Gram-negative analogs. The structure of an “adhesin” from the tip of the pneumococcal pilus (Izoré et al., 2010) reveals intradomain insertions of eukaryotic origin that may hold the key to systemic invasion.
E2 ubiquitin-conjugating enzymes catalyze the attachment of ubiquitin to lysine residues of target proteins. The UbcH5b E2 enzyme has been shown to play a key role in the initiation of the ubiquitination of substrate proteins upon action of several E3 ligases. Here we have determined the 2.2 Å crystal structure of an intermediate of UbcH5b∼ubiquitin (Ub) conjugate, which is assembled into an infinite...
Pili are fibrous virulence factors associated directly to the bacterial surface that play critical roles in adhesion and recognition of host cell receptors. The human pathogen Streptococcus pneumoniae carries a single pilus-related adhesin (RrgA) that is key for infection establishment and provides protection from bacterial challenge in animal infection models, but details of these roles remain unclear...
Mitochondrial ADP/ATP carriers are inhibited by two natural compounds, atractyloside (ATR) or carboxy-atractyloside (CATR), which differ by one carboxylate group. The interactions of the inhibitors with the carrier were investigated by single-molecule force spectroscopy. Transmembrane α helices of the ATR-inhibited carrier displayed heterogeneous mechanical and kinetic properties. Whereas α helix...
Single particle reconstruction from cryoelectron microscopy images, though emerging as a powerful means in structural biology, is faced with challenges as applied to asymmetric proteins smaller than megadaltons due to low contrast. Zernike phase plate can improve the contrast by restoring the microscope contrast transfer function. Here, by exploiting simulated Zernike and conventional defocused cryoelectron...
Perhaps 5%–10% of proteins bind to membranes via a covalently attached lipid. Posttranslational attachment of fatty acids such as myristate occurs on a variety of viral and cellular proteins. High-resolution information about the nature of lipidated proteins is remarkably sparse, often because of solubility problems caused by the exposed fatty acids. Reverse micelle encapsulation is used here to study...
Principal receptors for collagen, the most abundant component of the extracellular matrix (ECM), come from the integrin and discoidin domain (DDR) gene families. The latter are a class of receptor tyrosine kinases that bind to several collagens and mediate intracellular signaling. Carafoli et al. recently described a crystal structure of a DDR in complex with a trimeric collagen peptide ligand.
Poxviruses encode their own type IB topoisomerases (TopIBs), which release superhelical tension generated by replication and transcription of their genomes. To investigate the reaction catalyzed by viral TopIBs, we have determined the structure of a variola virus topoisomerase-DNA complex trapped as a vanadate transition state mimic. The structure reveals how the viral TopIB enzymes are likely to...
Neuronal Ca 2+ sensors (NCS) are high-affinity Ca 2+ -binding proteins critical for regulating a vast range of physiological processes. Guanylate cyclase-activating proteins (GCAPs) are members of the NCS family responsible for activating retinal guanylate cyclases (GCs) at low Ca 2+ concentrations, triggering synthesis of cGMP and recovery of photoreceptor cells to the dark-adapted...
The 5′ guanine-N7 cap is the first cotranscriptional modification of messenger RNA. In Saccharomyces cerevisiae, the first two steps in capping are catalyzed by the RNA triphosphatase Cet1 and RNA guanylyltransferase Ceg1, which form a complex that is directly recruited to phosphorylated RNA polymerase II (RNAP IIo), primarily via contacts between RNAP IIo and Ceg1. A 3.0 Å crystal structure of Cet1-Ceg1...
Bacteria produce a remarkable range of surface and secreted polysaccharides. Two pathways have been defined for the biosynthesis and export of capsular polysaccharides and exopolysaccharides in Gram-negative bacteria. A structure of AlgK described in this issue provides structural insight into a third previously unrecognized pathway associated with important biopolymers (Keiski et al., 2010).
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