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The baseplate of bacteriophage T4 is a multicomponent protein complex, which controls phage attachment to the host. It assembles from six wedges and a central hub. During infection the baseplate undergoes a large conformational change from a dome-shaped to a flat, star-shaped structure. We report the crystal structure of the C-terminal half of gene product (gp) 6 and investigate its motion with respect...
Acquired immunity in prokaryotes is achieved by integrating short fragments of foreign nucleic acids into clustered regularly interspaced short palindromic repeats (CRISPRs). This nucleic acid-based immune system is mediated by a variable cassette of up to 45 protein families that represent distinct immune system subtypes. CRISPR-associated gene 1 (cas1) encodes the only universally conserved protein...
KTN (RCK) domains are nucleotide-binding folds that form the cytoplasmic regulatory complexes of various K + channels and transporters. The mechanisms these proteins use to control their transmembrane pore-forming counterparts remains unclear despite numerous electrophysiological and structural studies. KTN (RCK) domains consistently crystallize as dimers within the asymmetric unit, forming...
Pyruvate carboxylase (PC) is a conserved metabolic enzyme with important cellular functions. We report crystallographic and cryo-electron microscopy (EM) studies of Staphylococcus aureus PC (SaPC) in complex with acetyl-CoA, an allosteric activator, and mutagenesis, biochemical, and structural studies of the biotin binding site of its carboxyltransferase (CT) domain. The disease-causing A610T mutation...
The localization of mRNAs in subcellular compartments is an efficient way to spatially restrict gene expression. Crystal structures of raver1-vinculin reported by Izard and coworkers now suggest a possible mechanism for mRNA localization during the assembly of focal adhesions.
Membrane compartments of manifold shapes are found in cells, often sculpted by cellular proteins. In particular, proteins of the BAR domain superfamily participate in membrane-sculpting processes in vivo and reshape also in vitro low-curvature membrane liposomes into high-curvature tubes and vesicles. Here we show by means of computer simulations totaling over 1 millisecond, how lattices involving...
In this issue, Batey and colleagues show that the purine riboswitch is able to bind purine analogs by exploiting various strategies, including lateral shifts of the bases and, most importantly, changes in ligand tautomeric form.
Mycobacteria have a unique cell wall consisting of mycolic acids, very-long-chain lipids that provide protection and allow the bacteria to persist within human macrophages. Inhibition of cell wall biosynthesis is fatal for the organism and a starting point for the discovery and development of novel antibiotics. We determined the crystal structures of KasA, a key enzyme involved in the biosynthesis...
Besides its function as an essential redox cofactor, nicotinamide adenine dinucleotide (NAD) also serves as a consumable substrate for several reactions with broad impact on many cellular processes. NAD homeostasis appears to be tightly controlled, but the mechanism of its regulation is little understood. Here we demonstrate that a previously predicted bacterial transcriptional regulator, NrtR, represses...
We recently determined the crystal structure of the functional core of human U1 snRNP, consisting of nine proteins and one RNA, based on a 5.5 Å resolution electron density map. At 5–7 Å resolution, α helices and β sheets appear as rods and slabs, respectively, hence it is not possible to determine protein fold de novo. Using inverse beam geometry, accurate anomalous signals were obtained from weakly...
Human DNA polymerase-ι (Polι) incorporates correct nucleotides opposite template purines with a much higher efficiency and fidelity than opposite template pyrimidines. In fact, the fidelity opposite template T is so poor that Polι inserts an incorrect dGTP approximately 10 times better than it inserts the correct dATP. We determine here how a template T/U is accommodated in the Polι active site and...
Mn 2+ -assisted catalysis by B. stearothermophilus TrpRS parallels that in polymerases and reduces specificity in amino acid activation. As predicted by nonequilibrium molecular dynamics simulations, multivariant thermodynamic cycles with [ATP]-dependent Michaelis-Menten kinetics and Mn 2+ for Mg 2+ substitution demonstrate energetic coupling of ATP affinities to the metal;...
The oxygen-dependent hydroxylation of proline residues in the α subunit of hypoxia-inducible transcription factor (HIFα) is central to the hypoxic response in animals. Prolyl hydroxylation of HIFα increases its binding to the von Hippel-Lindau protein (pVHL), so signaling for degradation via the ubiquitin-proteasome system. The HIF prolyl hydroxylases (PHDs, prolyl hydroxylase domain enzymes) are...
DsbD transmembrane protein dispatches electrons to periplasmic Trx/DsbE-like partners via specific interactions with its N-terminal domain, nDsbD. In the present study, PilB N-terminal domain (NterPilB) is shown to efficiently accept electrons coming from nDsbD from Neisseria meningitidis. Using an NMR-driven docking approach, we have modeled the structure of a mixed disulfide complex between NterPilB...
Hydroxylation of two proline residues in hypoxia inducible factor Hif-1α is a key step in the response to hypoxia. Here, Chowdury et al. (2009) elucidate the structural basis of this process by describing a structure for prolyl hydroxylase PHD2 bound to a peptide substrate.
Many neuropeptides and peptide hormones require amidation of their carboxy terminal for full biological activity. The enzyme peptidyl-α-hydroxyglycine α-amidating lyase (PAL; EC 4.3.2.5) catalyzes the second and last step of this reaction, N-dealkylation of the peptidyl-α-hydroxyglycine to generate the α-amidated peptide and glyoxylate. Here we report the X-ray crystal structure of the PAL catalytic...
In a recent issue of Molecular Cell, Das et al. (2009) show that the G2BR domain of gp78, a RING-family E3 ubiquitin ligase, binds the E2 Ube2g2 and induces conformational changes within Ube2g2 to allosterically enhance its interaction with cognate E3 RING domains.
The left-handed parallel β helix (LβH) fold has recently received attention as a possible structure for the prion protein (PrP) in its misfolded state. In light of this interest, we have developed an experimental system to examine the structural requirements of the LβH fold, using a known LβH protein, UDP-N-acetylglucosamine acyltransferase (LpxA), from E. coli. We showed that the β helix can tolerate...
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