Sandbox Reserved 196

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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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Contents 1 Introduction 2 Background 3 Biology of RNase B 4 Description 5 References 6 Additional Resources

Introduction

RNase B is a glycoprotein that can that cleave N-linked carbohydrates ^[1]. RNase B is structurally the same as RNase A. However is has an additional catalytic activity caused by the attachment of polysaccharrides at the Asn-34. 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].

Background

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

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

Biology of RNase B

Because RNase B has been crystallized to show that there are two units, slightly asymmetrical, 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 re 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.

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 Lys-41, His-12, and His-119 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. Ions can ligand to this Lys, and also to Arg-39 and Lys-1. 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 residue 15-23 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.

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Description

References

1. ↑ New England Bio Lab, INC http://www.neb.com/nebecomm/products/productP7817.asp
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

Additional Resources

• Dr. Johnson