Allosteric regulation of proteins by conformational change is a primary means of biological control. Traditionally it has been difficult to identify and characterize novel allosteric sites and ligands that freeze these conformational states. We present a site-directed approach using Tethering for trapping inhibitory small molecules at sites away from the active site by reversible disulfide bond...

24 European Crystallographic Meeting, ECM24, Marrakech, 2007 Page s126 Acta Cryst. (2007). A63, s126 Escherichia coli beta-galactosidase is known to be active only in the form of tetramers, while the cold-active Arthrobacter sp. C2-2 beta-galactosidase forms compact hexamers with active sites oriented into an internal cavity, connected by three types of channels with exterior solvent. Additiona...

Cytochrome P450 monooxygenases (CYPs/P450s) are heme-thiolate proteins whose role as a drug target against pathogenic microbes has been explored because of their stereo- and regio-specific oxidation activity. We aimed to assess the CYP53 family's role as a common alternative drug target against animal (including human) and plant pathogenic fungi and its role in fungal-mediated wood degradation....

Haloalkane dehalogenase (DhlA) hydrolyzes short-chain haloalkanes to produce the corresponding alcohols and halide ions. Release of the halide ion from the active-site cavity can proceed via a two-step and a three-step route, which both contain slow enzyme isomerization steps. Thermodynamic analysis of bromide binding and release showed that the slow unimolecular isomerization steps in the thre...

The recently discovered 150-cavity (formed by loop residues 147-152, N2 numbering) adjacent to the enzymatic active site of group 1 influenza A neuraminidase (NA) has introduced a novel target for the design of next-generation NA inhibitors. However, only group 1 NAs, with the exception of the 2009 pandemic H1N1 NA, possess a 150-cavity, and no 150-cavity has been observed in group 2 NAs. The r...

Phosphate and phosphate-containing buffers of physiological interest such as ATP and 3-phosphoglycerate were found to enhance catalysis by human carbonic anhydrase III (HCA III). Addition of phosphate caused an increase in both the catalyzed rate of hydration of CO2 at steady state measured by stopped-flow spectrophotometry and the exchange of 18O between CO2 and water at chemical equilibrium m...

Malate dehydrogenase specifically oxidizes malate to oxaloacetate. The specificity arises from three arginines in the active site pocket that coordinate the carboxyl groups of the substrate and stabilize the newly forming hydroxyl/keto group during catalysis. Here, the role of Arg-153 in distinguishing substrate specificity is examined by the mutant R153C. The x-ray structure of the NAD binary ...

Molecular surfaces often exhibit a complicated interior structure that is not fully visible from exterior viewpoints due to occlusion. In many cases this interior cavity is the most important feature of the surface. Applying standard blended transparency can reveal some of the hidden structure, but often results in confusion due to impaired surface-shape perception. We present ambient occlusion...

There are 9 serotypes of neuraminidase (NA) from influenza A virus (N1 to N9), which are classified into two groups based on primary sequences (groups 1 and 2). The structural hallmark of the two groups is the presence or absence of an extra 150-cavity (formed by the 150-loop) in the active site. Thus far, structures of NAs from 6 out of the 9 serotypes have been solved. Here, we solved the N5 ...

In the oxidized "ES" state of cytochrome c peroxidase, Trp-191 is reversibly oxidized to a stable cation free radical by the hypervalent heme. To explore the potential for engineering a binding site for heterocyclic compounds at this site, the mutant W191G was constructed. Two independent crystal structures of W191G at 2.1- and 2.3-A resolution show that W191G contains a well-defined, approxima...