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Ribofuranosyl Binding Protein

SBKB [doi:10.3942/psi_sgkb/fm_2011_6]
Featured System - June 2011
Short description: Molecular recognition is at the very heart of life.

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. Click on the image here to see an interactive Jmol that explores this unusual interaction and how it is recognized.

The JSmol tab below displays an interactive JSmol

Retinoblastoma Protein Pocket Domain (PDB entry 1gux)

Rb binds to many of its partners using a specific pocket that recognizes the motif LxCxE. The central domain of Rb is included in this structure, shown here in blue, with a short peptide bound in this pocket, with the backbone in green and the leucine-cysteine-glutamate in atomic colors. Use the buttons to switch the representation, and to get a close-up view of the pocket.


  1. 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)

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health