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| This Sandbox is Reserved from Feb 02, 2011, through Jul 31, 2011 for use by the Biochemistry II class at the Butler University at Indianapolis, IN USA taught by R. Jeremy Johnson. This reservation includes Sandbox Reserved 191 through Sandbox Reserved 200.
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Introduction
RNase B is a glycoprotein that can that cleave N-linked carbohydrates [1]. RNase B is structurally the same as RNase A, however it has an additional catalytic activity caused by the attachment of polysaccharrides at the . This small change allows RNase B to hydrolyze double-stranded RNA at ionic strengths where RNase A has no activity. This shows that small changes in the active sites of very similar molecules can lead to todally new roles and activities [2].
Structure and Biology of RNase B
RNase A and RNase B are statistically identical in their overall structure and amino acid make-up. However, as stated above, there is an important difference in that RNase B is bound to mannose carbohydrates. After undergoing tests, it has been found that this binding aids in the enthalpic
favorability, which leads to a kinetic stability that is 3 kJ/mol higher than RNase A
[3]. Even with RNase B being gycosylated, however, NMR data has shown that there isn't a significant difference in the protein conformations between RNase B and RNase A
[4]. There are slight differences that have been found through studying the crystal structure. Because RNase B crystallization has shown that there are two slightly asymmetrical units, the RNase has been examined to determine the active sites as well as other functions of the RNase B. The RNase B is made of two separate molecules, I and II, which are linked by a salt bridge of Asp-121 and Arg-85. This linkage determines the orientation of the two molecules in relation to one another. Not only does a salt bridge link this dimer-type molecule, but other ions also interact via cross-linkage to stabilize the structure
[2].
The crystallization of RNase B provided the structure of the active site in which double stranded RNA is hydrolyzed. The active site, a triangle formation of was shown to be the most intense active site and is found in both molecules I and II of RNase B. In molecule II, the most drastic difference is the proximity of the active site to Lys-66, because ions can ligand to . Even though both active sights are close to identical, the two separate molecules are packed very differently from one another. These active sights have been seen to deviate less from their “true” positions than those molecules in RNase A. Shown in the image, the region of (in top applet) appear to have more flexibility, and upon looking at the structure could provide the opening for the active site. This catalytic site, with all the structures shown, has still not been an aid in providing the mechanism by which RNase performs its duty of hydrolyzing double stranded RNA [2].
References
- ↑ New England Bio Lab, INC http://www.neb.com/nebecomm/products/productP7817.asp
- ↑ 2.0 2.1 2.2 Williams RL, Greene SM, McPherson A. The crystal structure of ribonuclease B at 2.5-A resolution. J Biol Chem. 1987 Nov 25;262(33):16020-31. PMID:3680242
- ↑ Imperiali B, O'Connor SE. Effect of N-linked glycosylation on glycopeptide and glycoprotein structure. Curr Opin Chem Biol. 1999 Dec;3(6):643-9. PMID:10600722
- ↑ Joao HC, Scragg IG, Dwek RA. Effects of glycosylation on protein conformation and amide proton exchange rates in RNase B. FEBS Lett. 1992 Aug 3;307(3):343-6. PMID:1322837
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