Sandbox Reserved 196

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	== Additional Resources ==		== Additional Resources ==
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Revision as of 16:58, 13 April 2011

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.

To get started: Click the edit this page tab at the top. Save the page after each step, then edit it again. Click the 3D button (when editing, above the wikitext box) to insert a 3D applet Jmol scene window. show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page. Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc. More help: Help:Editing

spinqualitylabelsall models 3D picture of RNase B dimer Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Contents 1 Introduction 2 Structure and Biology of RNase B 3 References 4 Additional Resources

Introduction

RNase B is a glycoprotein with N-linked carbohydrates ^[1]. RNase B is structurally the same as RNase A, however it has 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, showing that small changes in the active sites of very similar molecules can lead to totally new roles and activities ^[2].

Structure and Biology of RNase B

RNase A and RNase B have identical primary structures; however, RNase B is bound to mannose carbohydrates. This glycosylation increases the kinetic stability of RNase B by 3 kj/mol compared to RNase A ^[3]. Gycosylated, RNase B however, is not significantly different by NMR in protein

spinqualitylabelsall models Ribonuclease B with a strand of DNA in active site Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

conformation to RNase A ^[4].

Slight differences indclude changes in crystal packing. RNase B crystals have two slightly asymmetrical units. The crystals are dimeric with two separate molecules, I and II, which are linked by a salt bridge at 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

1. ↑ New England Bio Lab, INC http://www.neb.com/nebecomm/products/productP7817.asp
2. ↑ ^{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
3. ↑ 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
4. ↑ 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

Additional Resources

• http://www.pdb.org/pdb/explore/explore.do?structureId=1RBJ
• http://www.pdb.org/pdb/explore/explore.do?structureId=1RBB
• Ribonuclease
• User:R. Jeremy Johnson