Proteopedia - User contributions [en]

Sandbox Reserved 196

2011-04-15T12:20:59Z

Carissa Fuller:

{{Template:Johnson_CH462_Spring2011}}


<Structure load='1rbb' size='250' frame='true' align='right' caption='3D picture of RNase B dimer' scene='Sandbox_Reserved_196/Rbb_basic/1' name='1rbb' />

== Introduction ==

Ribonuclease B (RNase B) is a form of the enzyme RNase A that has an added glycoprotein with N-linked carbohydrates at <scene name='Sandbox_Reserved_196/Rbb_basic/16'>Asn-34</scene>, which means that the carbohydrate is attached at the <scene name='Sandbox_Reserved_196/Rbb_basic/17'>nitrogen</scene> of the Aspargine-34 side chain. This added sugar chain can aid in the folding of the protein as well as in cell to cell signaling<ref name="first">Varki A, Cummings RD, Esko JD, Freeze HH, Stanley P, Bertozzi CR, Hart GW, Etzler ME. ''Essentials of Glycobiology''. PMID:20301239</ref>. Glycoproteins also play an important role in tumor formation because it has been found that N-linked glycans recognized by the CD337 receptor on "natural killer cells" are mutated in tumor cells, stopping their death<ref name="second">http://en.wikipedia.org/wiki/Glycan</ref>. Other than the attachment of the polysaccharide, RNase B is structurally the same as RNase A, but the attachment allows for additional catalytic activity. 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 new roles and activities <ref name="third">PMID:3680242</ref>. <scene name='Sandbox_Reserved_196/Rbb_basic/1'>(Return to original scene)</scene>

== Structure and Biology of RNase B ==
[[Image:1RBJ.jpg | thumb|left|RNase B]]

Crystallization of RNase A and RNase B has shown that these two enzymes are identical in their<Structure load='1rbj' size='250' frame='true' align='right' caption='Molecule II of Ribonuclease B with a strand of DNA in active site' scene='Sandbox_Reserved_196/Secondary_structure/13' name ='1rbj' /> primary structure and amino acid makeup; however, RNase B has a single glycosylation at the <scene name='Sandbox_Reserved_196/Rbb_basic/18'>Asn-34</scene> site that differentiates RNase B from RNase A. RNase B has from five to nine mannose residues attached which can create a variance within RNase B molecules. This glycosylation increases the kinetic stability of the RNase B by 3 kJ/mol<ref name="fourth">PMID:10600722</ref>. This addition to RNase B, however, does not significantly change the protein conformation from RNase A<ref name="fifth">PMID:1322837</ref>.

Slight differences include changes in crystal packing, as the RNase B crystals have two slightly asymmetrical units. The crystals are <scene name='Sandbox_Reserved_196/Rbb_basic/1' target='1rbb'>dimeric</scene> (shown above) with two separate molecules, <scene name='Sandbox_Reserved_196/Rbb_basic/15' target='1rbb'>I</scene> and <scene name='Sandbox_Reserved_196/Rbb_basic/14' target='1rbb'>II</scene>, 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="third" />.

The crystallization of RNase B, in complex with sequence DNA, provided the structure of the active site when bound to nucleic acids. The active site, composed of <scene name='Sandbox_Reserved_196/Secondary_structure/15' target='1rbj'>His-12, Lys-41 and His-119</scene> and found in both molecules I and II of RNase B, is very similar to the active site of RNase A. A difference between RNase A and RNase B is <scene name='Sandbox_Reserved_196/Rbb_basic/19' target='1rbj'>residues 15-23</scene>, which are very flexible and can open up or close off the active site. Molecules I and II are slightly asymmetrical, and the most noticeable difference between the two is the position of the <scene name='Sandbox_Reserved_196/Secondary_structure/16'>Lys-66</scene>. This residue, which is present in both molecules, is much closer to the active site in molecule II. This is important because ions bind to Lys-66, like the DNA, making them accessible to the active site. While the crystalline packing of molecules I and II differ slightly, their active sites bind substrate in the same manner. Even though the crystallization of the structure has been successful, it has not been an aid to providing the mechanism by which RNase B has the catalytic activity to hydrolyze double stranded RNA.<ref name="third" />. <scene name='Sandbox_Reserved_196/Secondary_structure/13' target='1rbj'>(Return to original scene)</scene>

== References ==
<references />

== Additional Resources ==
<ref group="xtra">http://www.pdb.org/pdb/explore/explore.do?structureId=1RBJ</ref><ref group="xtra">http://www.pdb.org/pdb/explore/explore.do?structureId=1RBB</ref><ref group="xtra">[[Ribonuclease]]</ref><ref group="xtra">[[User:R. Jeremy Johnson]]</ref>
<references group="xtra"/>

File:1RBJ.jpg

2011-04-15T12:20:03Z

Carissa Fuller: uploaded a new version of "Image:1RBJ.jpg"

2011-03-29T21:30:58Z

Carissa Fuller:

Sandbox Reserved 196

2011-03-29T21:10:39Z

Carissa Fuller:

2011-03-29T15:32:29Z

Carissa Fuller:

Sandbox Reserved 196

2011-03-29T15:29:20Z

Carissa Fuller:

{{Template:Johnson_CH462_Spring2011}}


== Introduction ==

RNase B is a glycoprotein that can that cleave N-linked carbohydrates. 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.
== Background ==
[[Image:RNaseB.png | thumb|left|RNase B]]
3D pic (Right)
have at least 2 green links
<Structure load='1rbb' size='300' frame='true' align='right' caption='3D picture of RNase B dimer' scene='Sandbox_Reserved_196/Rbb_basic/1' />

<Structure load='1rbj' size='300' frame='true' align='right' caption='Ribonuclease B with a strand of DNA in active site' scene='Sandbox_Reserved_196/Secondary_structure/4' />

== Biology of RNase B ==
green links

== Description ==

== References ==

== Additional Resources ==
<ref group="xtra">Dr. Johnson</ref>
<references group="xtra"/>

2011-03-26T15:06:49Z

Carissa Fuller:

Sandbox Reserved 196

2011-03-26T15:00:35Z

Carissa Fuller:

Sandbox Reserved 196

2011-03-26T14:56:49Z

Carissa Fuller:

Sandbox Reserved 196

2011-03-26T14:29:33Z

Carissa Fuller:

Sandbox Reserved 196

2011-03-26T14:23:13Z

Carissa Fuller:

<Structure load='1rbb' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
{{Template:Johnson_CH462_Spring2011}}

<Structure load='1rbj' size='500' frame='true' align='right' caption='Insert caption here' scene='Sandbox_Reserved_196/Secondary_structure/4' />

Sandbox Reserved 196

2011-03-26T14:20:38Z

Carissa Fuller:

Sandbox Reserved 196

2011-03-25T15:09:49Z

Carissa Fuller:

Sandbox Reserved 196

2011-03-04T16:51:23Z

Carissa Fuller:

Sandbox Reserved 196

2011-03-04T16:45:52Z

Carissa Fuller:

<Structure load='1afu' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
{{Template:Johnson_CH462_Spring2011}}

User:Carissa Fuller

2011-02-21T21:19:39Z

Carissa Fuller:

Carissa Fuller and Emily Fischer are students in CH462 at Butler University with Dr. R. Jeremy Johnson. They are both Chemistry/Pre-Med majors, and are currently juniors.