Metal ions are essential cofactors for various ribozymes. Here we dissect the roles of metal ions in an aminoacyl-tRNA synthetase-like ribozyme (ARS ribozyme), which was evolved in vitro. This ribozyme can charge phenylalanine on tRNA in cis, where it is covalently attached to the 5'-end of tRNA (i.e. a form of precursor tRNA), as well as in trans, where it can act as a catalyst. The presence o...

Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor M...

Metal–alkane binding energies have been calculated for [CpRe(CO)2](alkane) and [(CO)2M(C5H4)C'C(C5H4)M(CO)2](alkane), where M Re or Mn. Calculated binding energies were found to increase with the number of metal–alkane interaction sites. In all cases examined, the manganese–alkane binding energies were predicted to be significantly lower than those for the analogous rhenium–alkane complexes. Th...

The structure of a protein determines its function and its interactions with other factors. Regions of proteins that interact with ligands, substrates, and/or other proteins, tend to be conserved both in sequence and structure, and the residues involved are usually in close spatial proximity. More than 70,000 protein structures are currently found in the Protein Data Bank, and approximately one...

Metal-binding sites have been engineered into both de novo designed and naturally occurring proteins. Although the redesign of existing metal-binding sites in naturally occurring proteins still offers the most promise for a successful design, the more challenging goal of engineering metal-binding sites in de novo designed proteins and peptides is being achieved with increasing frequency. Creati...

Pyruvate kinase (EC 2.7.1.40) is inhibited by phenethylbiguanide. The kinetics of inhibition are competitive between biguanide and divalent, but not monovalent, metal cation activators of the enzyme; biguanide inhibition thus resembles inhibition by Ca(++). Alteration of either the polar or nonpolar portion of the phenethylbiguanide molecule quantitatively reduces its effectiveness as an inhibi...

A novel hybrid of azacrown ether-oxabridged fluorogenic chemosensor (1) has been synthesized: the metal ion binding ability of the hybrid molecule shows higher affinity towards transition metal ion Zn(2+) and heavy metal ion Hg(2+) compared to the parent azacrown ether which shows poor metal ion selectivity: the binding modes of the Zn(2+) and Na(+) towards have been discussed.

Metal ions play a critical role in living systems. About one third of proteins need to bind metal for their stability and/or function. In this review, current sequence based and structure based methods for metal binding site prediction will be presented, with emphasis on the CHED and SeqCHED methods of prediction from apo-protein structures and protein sequences having homologs (even remote) in...

The tetrahedral Cys2His2 Zn(II)-binding site in the de novo designed protein Z alpha 4 [Regan, L., & Clarke, N. D. (1990) Biochemistry 29, 10878] has been studied by independently mutating each of the metal-binding ligands to alanine. The contribution of each ligand to the geometry and affinity of metal binding has been characterized using Co(II), Zn(II), and Cd(II). The results indicate that a...

BACKGROUND Metal ions participate in the three-dimensional folding of RNA and provide active centers in catalytic RNA molecules. The positions of metal ions are known for a few RNA structures determined by X-ray crystallography. In addition to the crystallographically identified sites, solution studies point to many more metal ion binding sites around structured RNAs. Metal ions are also presen...