Visualizing Enzyme Structures

In the Chapter 19 Lagniappe, we discussed how to access enzyme structural data from the Protein Data Bank. Once the data for a specific enzyme have been located, it s then possible to visualize, manipulate, and study the structure. You can do this either by downloading the data file to your own computer and opening it with a free visualization program, such as DeepView (Swiss PDB Viewer) 

Let s say that you want to study one of the more complex and interesting amino acid catabolic pathways and that you need to view urocanase, a key enzyme in histidine catabolism that catalyzes the addition of water to trans-urocanate. 

Explore on your own there is an immense amount of detailed information you can learn. 

FIGURE 20.14 An image of urocanase, downloaded from the Protein Data Bank. Urocanase is a dimer composed oftwo identical subunits. 

10 What amino acid is the following a-keto acid derived from  

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There is perhaps more three-dimensional structural information available on thrombin than any other enzyme. We will study selected examples of the use of such information, indicating the relevant Protein Data Bank (http //www.rcsb.org/ pdb/) entries [labcj for those who wish to visualize the structures in 3-D. 

Computers facilitate the design of new enzyme inhibitors by enabling scientists to graphically visualize the structure of targeted molecules. 

In order to get the activated amino acid incorporated into peptide linkage it is necessary to get it off the activating enzyme in the form of a carboxyl derivative. This, however, is no easy matter, since we not only have to avoid phosphorylation reactions by the adenylyl group, but most likely we would also have to displace the PP from the enzyme surface before the acyl acceptor could get access to the reactive group. Nothing poffltive is known about the mechanism of this transfer, but it might be useful to visualize the structural requirements of such an acceptor. First, in order to displace the pyrophosphate and get the acceptor bound to the... 

Figure 2.10 Secondary and tertiary structure of the copper enzyme azurin visualized using Wavefunction, Inc. Spartan 02 for Windows from PDB data deposited as 1JOI. See text for visualization details. Printed with permission of Wavefunction, Inc., Irvine, CA. (See color plate.)...

Figure 2.10 Secondary and tertiary structure of the enzyme lysozyme, PDB 2C80. Visualized using Cambridge Soft Chem3D Ultra 10.0 with notations in ChemDraw Ultra 10.0. ChemDraw Ultra, version 10.0. (Printed with permission of CambridgeSoft...

The terminal complex hypothesis proposes that the cellulose synthesizing enzyme complex can be visualized with electron microscopy. Terminal complex is the name given to collections of plasma membrane particles thought to represent the cellulose synthase. While direct evidence is still not available to support this hypothesis, the amount of indirect supporting evidence has grown dramatically in the past few years. The relationship between terminal complexes, cellulose physical structure and the biochemical events of cellulose biosynthesis will be discussed. 

The terminal complex hypothesis proposes that structural manifestations of the cellulose synthase enzyme complex can be visualized with the freeze fracture specimen preparation technique for electron microscopy. These... 

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