Sandbox Reserved 196: Difference between revisions
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== Introduction == | == Introduction == | ||
RNase B is a glycoprotein | RNase B is a glycoprotein with 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 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, showing that small changes in the active sites of very similar molecules can lead to totally 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 == | ||
[[Image:RNaseB.png | thumb|left|RNase B]] | [[Image:RNaseB.png | thumb|left|RNase B]] | ||
RNase A and RNase B | RNase A and RNase B have identical primary structures; however, RNase B is bound to mannose carbohydrates. This glycosylation increases the <Structure load='1rbj' size='250' frame='true' align='right' caption='Ribonuclease B with a strand of DNA in active site' scene='Sandbox_Reserved_196/Secondary_structure/8' name ='1rbj' />kinetic stability of RNase B by 3 kj/mol compared to RNase A <ref name="third">PMID:10600722</ref>. Gycosylated, RNase B however, is not significantly different by NMR in protein conformation to RNase A <ref name="fourth">PMID:1322837</ref>. | ||
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 <ref name="second" />. | |||
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> | 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> | ||
