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Structural and kinetic evidence points to an induced loop movement in thymidylate kinase as leading to the limiting step in AZT activation in HIV therapy.
The structure of an RNA aptamer targeted against the aromatic compound theophylline yields a treasure of stereochemical information, emphasizing the versatility of RNA aptamers in their interaction with a plethora of different molecules.
Structural comparison of thymidylate kinase complexed with either dTMP or with AZTMP suggests that the low phosphorylation rate of AZTMP is due to an induced P-loop movement.
The three N-terminal zinc fingers of transcription factor IIIA bind in the DNA major groove. Substantial packing interfaces are formed between adjacent fingers, the linkers lose their intrinsic flexibility upon DNA binding, and several lysine side chains implicated in DNA recognition are dynamically disordered.
The Ras-interacting domains of the the protein-kinase Raf and the Ral guanine nucleotide dissociation stimulator, RalGDS, lack extensive sequence similarity, but their overall three-dimensional structures are very similar to each other. Mutational analysis indicated that three residues in the RalGDS domain are critical for its interaction with Ras.
The crystal structure of the fructose-2,6-bisphosphatase domain trapped during the reaction reveal a phosphorylated His 258, and a water molecule immobilized by the product, fructose-6-phosphate. The geometry suggests that the dephosphorylation step requires prior removal of the product for an ‘associative in-line’ phosphoryl transfer to the catalytic water.
Using a mutant version of E. coli alkaline phosphatase, we succeeded in trapping and determining the structure of the phospho-enzyme intermediate. The X-ray structure also revealed the catalytic water molecule, bound to one of the active site zinc ions, positioned ideally for the apical attack necessary for the hydrolysis of the intermediate.
The predicted distribution of globular proteins over folding types in five complete genomes differs from the tendencies observed in known protein structures. The ratio between the number of predicted membrane and globular proteins is conserved.
