Sandbox Reserved 196

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== Introduction ==
== Introduction ==
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RNase B is a glycoprotein that can that cleave N-linked carbohydrates <ref>New England Bio Lab, INC http://www.neb.com/nebecomm/products/productP7817.asp</ref>. RNase B is structurally the same as RNase A, however it has an additional catalytic activity caused by the attachment of polysaccharrides at the <scene name='Sandbox_Reserved_196/Rbb_basic/5'>Asn-34</scene>. 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 <ref>PMID:3680242</ref>. <scene name='Sandbox_Reserved_196/Rbb_basic/1'>(Return to original scene)</scene>
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RNase B is a glycoprotein that can that cleave N-linked carbohydrates <ref name="first">New England Bio Lab, INC http://www.neb.com/nebecomm/products/productP7817.asp</ref>. RNase B is structurally the same as RNase A, however it has an additional catalytic activity caused by the attachment of polysaccharrides at the <scene name='Sandbox_Reserved_196/Rbb_basic/5'>Asn-34</scene>. 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 <ref name="second">PMID:3680242</ref>. <scene name='Sandbox_Reserved_196/Rbb_basic/1'>(Return to original scene)</scene>
== Structure and Biology of RNase B ==
== Structure and Biology of RNase B ==
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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 <scene name='Sandbox_Reserved_196/Secondary_structure/11' target='1rbj'>Lys-41, His-12, and His-119</scene> 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 <scene name='Sandbox_Reserved_196/Secondary_structure/10' target='1rbj'>Lys-66, Arg-39 and Lys-1</scene>. 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 <scene name='Sandbox_Reserved_196/Rbb_basic/2' target='1rbb'>residues 15-23</scene> (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. <scene name='Sandbox_Reserved_196/Secondary_structure/8' target='1rbj'>(Return to original scene)</scene>
+
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 <scene name='Sandbox_Reserved_196/Secondary_structure/11' target='1rbj'>Lys-41, His-12, and His-119</scene> 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 <scene name='Sandbox_Reserved_196/Secondary_structure/10' target='1rbj'>Lys-66, Arg-39 and Lys-1</scene>. 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 <scene name='Sandbox_Reserved_196/Rbb_basic/2' target='1rbb'>residues 15-23</scene> (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 <ref name="second" />. <scene name='Sandbox_Reserved_196/Secondary_structure/8' target='1rbj'>(Return to original scene)</scene>

Revision as of 21:30, 29 March 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.
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3D picture of RNase B dimer

Drag the structure with the mouse to rotate

Contents

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

Image:RNaseB.png
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 are linked by a salt bridge of Asp-121

Ribonuclease B with a strand of DNA in active site

Drag the structure with the mouse to rotate
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 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 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
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