Sandbox Reserved 194

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Further binding pocket characterization was accomplished using the oglionucleotide <scene name='Sandbox_Reserved_194/1rcn_just_dtda/1'>d(ApTpApApG)</scene>.
Further binding pocket characterization was accomplished using the oglionucleotide <scene name='Sandbox_Reserved_194/1rcn_just_dtda/1'>d(ApTpApApG)</scene>.
While binding of other nucleobases to the B2 and B3 sites is possible, the imaging of this <scene name='Sandbox_Reserved_194/1rcn_structure/2'>complex </scene>elucidated the preferences
While binding of other nucleobases to the B2 and B3 sites is possible, the imaging of this <scene name='Sandbox_Reserved_194/1rcn_structure/2'>complex </scene>elucidated the preferences
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for adenosine bases at these two positions. RNase A establishes <scene name='Sandbox_Reserved_194/1rcn_his/6'>pi stacking between His119 and A3 </scene>in addition to hydrogen bonding between <scene name='Sandbox_Reserved_194/1rcn_hydrogen_bonding/4'>Asn71-A3, Gln69-A3 and Gln69-A4</scene>. ‘<ref>PMID:8063789</ref>’
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for adenosine bases at these two positions. RNase A establishes <scene name='Sandbox_Reserved_194/1rcn_his/7'>pi stacking between His119 and A3 </scene>in addition to hydrogen bonding between <scene name='Sandbox_Reserved_194/1rcn_hydrogen_bonding/4'>Asn71-A3, Gln69-A3 and Gln69-A4</scene>. ‘<ref>PMID:8063789</ref>’
== References ==
== References ==
<references/>
<references/>

Revision as of 22:50, 12 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.
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Ribonuclease A Substrate Binding

Thymidylic acid tetramer and ApTpApApG complexed with ribonuclease A showing pi stacking and hydrogen bonding

Drag the structure with the mouse to rotate

RNA degradation and formation is essential in protein regulation within the body. RNase A is an endonuclease that cleaves and breaks down RNA through attack at its 2’OH. It has served as a model providing insight into the stability, folding and chemistry of proteins. ‘[1]’ ‘[2]’

Image:RTAsurface2.png
Thymidylic acid tetramer complexed with ribonuclease A


To determine the structural characteristics of RNA substrate binding to RNase A, X-ray crystallography was used to image inhibitory DNA tetramers bound to the enzyme. DNA lacks the 2′OH essential to RNA cleavage, making the complex more conducive to crystallography. In previous studies, has provided information into the specificity of the binding pocket subunits, B0, B1, B2 and B3. Many interactions observed in this complex occur between amino acid residues and the nucleic acid backbone such as hydrogen bonding between the . Because of the interactions with the , it appears this site is exclusive to pyrimidines. ‘[3]’

Image:RCNsurface2.png
ApTpApApG complexed with ribonuclease A


Further binding pocket characterization was accomplished using the oglionucleotide . While binding of other nucleobases to the B2 and B3 sites is possible, the imaging of this elucidated the preferences for adenosine bases at these two positions. RNase A establishes in addition to hydrogen bonding between . ‘[4]’


References

  1. ↑ Raines RT. Ribonuclease A. Chem Rev. 1998 May 7;98(3):1045-1066. PMID:11848924
  2. ↑ Leonidas, Demetres. "Ribonuclease A." 1997.
  3. ↑ Birdsall DL, McPherson A. Crystal structure disposition of thymidylic acid tetramer in complex with ribonuclease A. J Biol Chem. 1992 Nov 5;267(31):22230-6. PMID:1429575
  4. ↑ Fontecilla-Camps JC, de Llorens R, le Du MH, Cuchillo CM. Crystal structure of ribonuclease A.d(ApTpApApG) complex. Direct evidence for extended substrate recognition. J Biol Chem. 1994 Aug 26;269(34):21526-31. PMID:8063789
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