To dissect the effects of the nucleotide-binding and catalytic metal ions on DNA polymerase mechanisms for DNA repair and synthesis, aside from the chemical reaction, we investigate their roles in the conformational transitions between closed and open states and assembly/disassembly of the active site of polymerase /DNA complexes before and after the chemical reaction of nucleotide incorporatio...

In this paper, catalytic oxidation of CO over the LaFe1-xCuxO3 (x= 0, 0.2, 0.4, 0.6) perovskite-type oxides was investigated. The catalysts were synthesized by sol-gel method and characterized by XRD, BET, FT-IR, H2-TPR and SEM methods. The catalytic activity of catalysts was tested in catalytic oxidation of CO. XRD patterns confirmed the synthesized perovskites to be single-phase perovskite-ty...

Previous studies with beef heart mitochondrial F1 ATPase suggest a mechanism in which binding of substrate (ATP) at one catdytic site accelerates the release of products (ADP + Pi) from a separate catalytic site. hitid velocity studies reported here, in harmony with this mechanism, show a biphasic rate response with apparent K,,, values of 250 and 1.7 PM and V,, values of 54 and 2.2 pmol/min/mg...

Members of the RNase III family are the primary cellular agents of dsRNA (double-stranded RNA) processing. Bacterial RNases III function as homodimers and contain two dsRBDs (dsRNA-binding domains) and two catalytic sites. The potential for functional cross-talk between the catalytic sites and the requirement for both dsRBDs for processing activity are not known. It is shown that an Escherichia...

The rational design of a set of hemin/G-quadruplex (hGQ)–dopamine binding aptamer (DBA) conjugates, acting as nucleoapzymes, is described. The nucleoapzyme constructs consist of a hGQ DNAzyme as a catalytic unit and DBA as a substrate binding unit that are brought into spatial proximity by a duplex scaffold composed of complementary oligonucleotide strands. When the hGQ unit is linked to the du...

The FireDB database is a databank for functional information relating to proteins with known structures. It contains the most comprehensive and detailed repository of known functionally important residues, bringing together both ligand binding and catalytic residues in one site. The platform integrates biologically relevant data filtered from the close atomic contacts in Protein Data Bank cryst...

Little is known about the reorganization capacity of water molecules at the active sites of enzymes and how this couples to the catalytic reaction. Here, we study the dynamics of water molecules at the active site of a highly proficient enzyme, Δ(5)-3-ketosteroid isomerase (KSI), during a light-activated mimic of its catalytic cycle. Photoexcitation of a nitrile-containing photoacid, coumarin18...

BACKGROUND Helicobacter pylori is the etiologic agent of common gastritis and a risk factor for gastric cancer. It is also one of the richest sources of Type II restriction-modification (R-M) systems in microorganisms. PRINCIPAL FINDINGS We have cloned, expressed and purified a new restriction endonuclease HpyAV from H. pylori strain 26695. We determined the HpyAV DNA recognition sequence and...

F(1)-ATPase is a rotary molecular motor in which the central gamma subunit rotates inside a cylinder made of alpha(3)beta(3) subunits. To clarify how ATP hydrolysis in three catalytic sites cooperate to drive rotation, we measured the site occupancy, the number of catalytic sites occupied by a nucleotide, while assessing the hydrolysis activity under identical conditions. The results show hithe...