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Ribofuranosyl Binding Protein

June 2011

Molecular recognition is at the very heart of life. Genetic information is transmitted through the specific interaction of bases. Using an array of specific contacts, enzymes force molecules into the conformation needed to catalyze a reaction. Receptors recognize hormones, viruses recognize receptors, and antibodies recognize viruses. Structural biology has revealed the atomic basis of this specificity, showing the many biological tricks-of-the-trade used in molecular interaction.

Periplasmic Binding Proteins

Periplasmic binding proteins have a specific job. They float around in the space between the two membranes surrounding a bacterial cell, searching for a particular type of molecule. When they find one, they capture it and deliver it to transporters at the inner membrane. Some search for ions, others for vitamins, and others for nutrients and food molecules. The one shown here, solved by researchers at NYSGXRC and available in PDB entry 3ksm, binds to ribose sugars. Like many of this class of protein, it is composed of two domains connected by a flexible linker, which traps the sugar inside.

Trapping Molecules

The two-domain structure of the protein is perfect for its job. Since the sugar is trapped inside, the protein can examine it from all sides. This is particularly important for sugars, since they are bristling with hydroxyl groups, and many different sugars look much the same. The two-domain structure is also good for the delivery of its cargo. When the protein has captured a sugar, the transporter recognizes its closed structure. Then, the transporter can pry it open to release the sugar.

Sugar Specificity

Ribofuranosyl binding protein uses several tricks to recognize its target sugar. First of all, it has an array of hydrogen-bonding groups to grip the many hydroxyl groups of the sugar. It also has two aromatic amino acids that contact regions of the sugar where carbon atoms are exposed. The crystal structure revealed that this protein favors an unusual conformation of the ribose ring.

Image
JSmol

Ribose Binding Proteins (PDB entries 3ksm and 1dbp)

The ribose sugar bound to ribofuranosyl binding protein adopts a furanose conformation, forming a five-membered ring. You can compare this to a related structure of ribose with ribose binding protein, where the sugar adopts a six-membered pyranose ring, which is the typical conformation found in periplasmic sugar binding proteins. Both proteins form many hydrogen bonds (shown with thin bonds) to the sugar hydroxyl groups. However, ribose binding protein has three aromatic side chains (shown in turquoise) surrounding the binding site, and ribofuranosyl binding protein has only two. By reducing the amount of aromatic contact, ribofuranosyl binding protein favors the smaller ring conformation of the sugar.

Full size ribbon diagram

References

Bagaria, A., Kumaran, D., Burley, S.K. & Swaminathan, S. Structural basis for a ribofuranosyl binding protein: insights into the furanose specific transport. Proteins 79, 1352-1357 (2011)