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Catalysis by radical enzymes dependent on coenzyme B12 (AdoCbl) relies on the reactive primary 5′‐deoxy‐5′adenosyl radical, which originates from reversible Co−C bond homolysis of AdoCbl. This bond homolysis is accelerated roughly 1012‐fold upon binding the enzyme substrate. The structural basis for this activation is still strikingly enigmatic. As revealed here, a displaced firm adenosine binding cavity in substrate‐loaded glutamate mutase (GM) causes a structural misfit for intact AdoCbl that is relieved by the homolytic Co−C bond cleavage. Strategically interacting adjacent adenosine‐ and substrate‐binding protein cavities provide a tight caged radical reaction space, controlling the entire radical path. The GM active site is perfectly structured for promoting radical catalysis, including "negative catalysis", a paradigm for AdoCbl‐dependent mutases. [ABSTRACT FROM AUTHOR]

The biochemical characterization of the purified protein is reported demonstrating that YcnD is an FMN-containing enzyme that can be reduced by NADH or NADPH. The findings suggest that NADPH is the physiological reductant of the enzyme.

The solvation and structure of aquocobalamin (vitamin B12a, I+) in crystal and aqueous solutions are determined. The EXAFS spectra of the aquocobalamin, perchlorate, 1+ClO(super -)(sub 4), crystals exhibits that, both in solid state and in solution, the coordination of cobalt is same. The single crystal structure analysis shows that 1+ClO(super -)(sub 4) crystallizes in the orthorhombic space group P212121, with approximately 100 solvent water molecules for each unit cell and four 1+ClO4 moieties. In aquocobalamin chloride, an intramolecular hydrogen bonds to the Co(III) axially coordinated water molecule, as given by the nuclear magnetic resonance data.

Supplementation of imidazole to growing cells of Propionibacterium shermanii yields Co(beta)-cyanoimidazolylcobamide. NMR and X-ray crystallographic studies help analyze the compound structure. A comparison with vitamin B12 reveals structural differences and helps examine the influence of the 5, 6-dimethylbenzimidazole base. Removal of imidazole by this base increases the Co-N(ax) bond length, enhances folding of corrin ring and causes a tilt in the cobalt-oriented nucleotide base.

A newly developed nuclear magnetic resonance (NMR) technique for the structural modelling of relatively small molecules was presented. The technique involved two-dimensional analyses in conjunction with distance geometry and Overhauser effect back-calculational methods. Structural assignments were provided by heteronuclear multiple quantum coherence and heteronuclear multiple bond spectroscopies. A sample study involving the 12,13-diepimeric F430 coenzyme showed that the structure derived from the NMR technique correlated with X-ray structural studies.

Abstract Background Structural data from crystallographic analyses contain a vast amount of information on protein-protein contacts. Knowledge on protein-protein interactions is essential for understanding many processes in living cells. The methods to investigate these interactions range from genetics to biophysics, crystallography, bioinformatics and computer modeling. Also crystal contact information can be useful to understand biologically relevant protein oligomerisation as they rely in principle on the same physico-chemical interaction forces. Visualization of crystal and biological contact data including different surface properties can help to analyse protein-protein interactions. Results VASCo is a program package for the calculation of protein surface properties and the visualization of annotated surfaces. Special emphasis is laid on protein-protein interactions, which are calculated based on surface point distances. The same approach is used to compare surfaces of two aligned molecules. Molecular properties such as electrostatic potential or hydrophobicity are mapped onto these surface points. Molecular surfaces and the corresponding properties are calculated using well established programs integrated into the package, as well as using custom developed programs. The modular package can easily be extended to include new properties for annotation. The output of the program is most conveniently displayed in PyMOL using a custom-made plug-in. Conclusion VASCo supplements other available protein contact visualisation tools and provides additional information on biological interactions as well as on crystal contacts. The tool provides a unique feature to compare surfaces of two aligned molecules based on point distances and thereby facilitates the visualization and analysis of surface differences.

Several studies are conducted to explain the 3D structure of the FAD-dependent hydronitrile lyase (HNL) that is obtained from almond with the presence of benzaldehyde in its active site. The reasons behind the absence of the dehydrogenation activity in the cyanohydrin formation mechanism are also discussed.

The X-ray structural characterization of imidazolylcobalamin (ImCbl) and histitinylcobalamin (HisCbl) are described. The results have shown that the conformational change of the protein from an open form is important in [B.sub.12] trafficking and/or provide a mechanism by which extracellular surface transcobalamin (TC) receptors can distinguish between the various Cbl forms of holo-TC.