Sandbox Reserved 195: Difference between revisions

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<Structure load='1RNU' size='500' frame='true' align='right' caption='RNase S (PDB: 1RNU) is a protein composed of 2 fragments:  S Peptide (residues 1-20) and S Protein (residues 21-124).  It is a result of cleavage of RNase A between residues 20 and 21.' scene='Insert optional scene name here' target='0' />


[[Image:surface view of rnase s.png|200px|left|thumb|  The image above depicts the surface interaction between the S peptide and S protein fragments; S peptide is blue, S protein is yellow.]]




RNase A and RNase S have very similar structures except for a few key areas, one being the cleavage site (residues 16-23)<ref name="Raines"> PMID:11848924</ref>.  Decreased order in these amino acids is seen in RNase S.  The <scene name='Sandbox_Reserved_195/Clevage_site/1' target='1'>cleavage site</scene> on RNase A is located between residues Ala 20 and Ser 21.  Upon cleavage, the fragments S peptide and S protein are created, giving RNase S its unique structure.  <scene name='Sandbox_Reserved_195/S_peptide/1' target='0'>S Peptide</scene> consists of residues 1-20, and is largely responsible for proper folding.  S protein is comprised of residues 21-124.  Additionally, RNase A and RNase S have many conserved structural components, as they are essentially the same protein.  Glutamine 60 is a highly conserved amino acid throughout many different species, showing its importance in both <scene name='Sandbox_Reserved_195/Gln_60/2' target='0'>RNase S</scene> and <scene name='Sandbox_Reserved_195/Glutamine_60_rnase_a/1' target='1'>RNase A</scene>.  Glu 60 is also interesting, because it is the only residue in an unfavorable position (Φ= -100, ψ= -130) as defined in the Ramachandran plot <ref name="Kim">PMID:1463719</ref>. 


RNase A and RNase S have very similar structures except for a few key areas, one being the cleavage site (residues 16-23)<ref name="Raines"> PMID:11848924</ref>.  Decreased order in these amino acids is seen in RNase S.  The <scene name='Sandbox_Reserved_195/Clevage_site/4' target='1'>cleavage site</scene> on RNase A is located between residues Ala 20 and Ser 21.  Upon cleavage, the fragments S peptide and S protein are created, giving RNase S its unique structure.  <scene name='Sandbox_Reserved_195/S_peptide/8' target='0'>S Peptide</scene> consists of residues 1-20, and is largely responsible for proper folding.  <scene name='Sandbox_Reserved_195/S_protein/2'>S protein</scene> is comprised of residues 21-124.  Additionally, RNase A and RNase S have many conserved structural components, as they are essentially the same protein.  Glutamine 60 is highly conserved structurally between  <scene name='Sandbox_Reserved_195/Gln_60/3' target='0'>RNase S</scene> and <scene name='Sandbox_Reserved_195/Glutamine_60_rnase_a/5' target='1'>RNase A</scene>, as well as in many different species, demonstrating its importance.  Glu 60 is also interesting, because it is the only residue in an unfavorable position (Φ= -100, ψ= -130) as defined in the Ramachandran plot <ref name="Kim">PMID:1463719</ref>. 




The <scene name='Sandbox_Reserved_195/Active_site/1' target='0'>active site</scene> of RNase S consists of residues His 12, Lys 41, Val 43, Asn 44, Thr 45, His 119, Phe 120, Asp 121, and Ser 123.  Residues 1, 15-20, 21-23, and 124 could be removed without serious consequence to the structure or activity of RNase S.  Residue 124 could also be removed from RNase A without compromising the structure. <ref name="Wyckoff et al">PMID:6037556</ref>




<Structure load='7rsa' size='500' frame='true' align='left' caption='RNase A (PDB: 7rsa), also known as bovine pancreatic ribonuclease A, has been studied for years to learn about protein structure, stability, and folding.' scene='Insert optional scene name here' target='1' />
<Structure load='1RNU' size='500' frame='true' align='right' caption='RNase S (PDB: 1RNU) is a protein composed of 2 fragments:  S Peptide (residues 1-20) and S Protein (residues 21-124).  It is a result of cleavage of RNase A between residues 20 and 21.' scene='Sandbox_Reserved_195/Ribonuclese_s_basic/3' target='0' />




The <scene name='Sandbox_Reserved_195/Active_site/2' target='0'>active site</scene> of RNase S consists of <scene name='Sandbox_Reserved_195/Active_site/3'>residues</scene> His 12, Lys 41, Val 43, Asn 44, Thr 45, His 119, Phe 120, Asp 121, and Ser 123. <scene name='Sandbox_Reserved_195/His_12/1'>His 12</scene> is the only residue in the active site that is located on the S peptide fragment. <scene name='Sandbox_Reserved_195/Lys_41_and_his_119/1'>Lys 41 and His 119</scene> are also crucial to the functioning of RNase S.  Interestingly, both catalytic Histidines perform the same function, even though they are located on <scene name='Sandbox_Reserved_195/Histines_and_lysines/2'>different fragments</scene>.  Residues 1, 15-20, 21-23, and 124 could be removed without serious consequence to the structure or activity of RNase S.  Residue 124 could also be removed from RNase A without compromising the structure. <ref name="Wyckoff et al">PMID:6037556</ref>






<Structure load='7rsa' size='500' frame='true' align='left' caption='RNase A (PDB: 7rsa), also known as bovine pancreatic ribonuclease A, has been studied for years to learn about protein structure, stability, and folding.' scene='Sandbox_Reserved_195/Ribonuclease_a_basic/3' target='1' />




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Hydrogen bonding and hydrophobic interactions play a major role in the structure of RNase S. <ref name="Kim" /> There are 84 water molecules present, with 8 of these specifically connecting S peptide and S protein.  Some of these water molecules are also conserved throughout all RNase derivatives.  Hydrophobic interactions between residues Phe 8, Met 13, His 12, Ala 4 are essential in holding the S Peptide in place.  In addition to these residues, Asp 14 is also important in peptide-protein binding, as represented in the 2D picture.  In the picture, it appears that the protein and peptide are not connected; this is because the bond cleavage between residues 20 and 21 of RNase A has already occurred.  Additionally RNase S has a rigid hydrophobic core; one-third of the surface of the core is made up of the S peptide.  The surrounding loops have more flexibility. 




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[[Image:asp14.png]]


                                                                                                                        {{Quote box
 
  | quote = Residue Asp 14 which aids in S peptide - S protein bond formation.
 
  | source =
Hydrogen bonding and hydrophobic interactions play a major role in the structure of RNase S. <ref name="Kim" /> There are 84 water molecules present, with 8 of these specifically connecting S peptide and S protein. Some of these water molecules are also conserved throughout all RNase derivatives. Hydrophobic interactions between residues Phe 8, Met 13, His 12, Ala 4 are essential in holding the S Peptide in place.  In addition to these residues, <scene name='Sandbox_Reserved_195/Asp_14/4'>Asp 14</scene> is also important in peptide-protein binding.  In the picture, it appears that the protein and peptide are not connected; this is because the bond cleavage between residues 20 and 21 of RNase A has already occurred.  Additionally RNase S has a rigid hydrophobic core; one-third of the surface of the core is made up of the S peptide. The surrounding loops have more flexibility.  
  | width =10
 
| align  =Left
 
}}
 








Conclusion??


[[References ]]
[[References ]]
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RNase S on PDB: http://www.rcsb.org/pdb/explore/explore.do?structureId=1RNU
RNase S on PDB: http://www.rcsb.org/pdb/explore/explore.do?structureId=1RNU


RNase A on PDB:
RNase A on PDB: http://www.rcsb.org/pdb/explore/explore.do?structureId=7RSA


Ribonuclease on Proteopedia: http://proteopedia.org/wiki/index.php/Ribonuclease
Ribonuclease on Proteopedia: http://proteopedia.org/wiki/index.php/Ribonuclease

Latest revision as of 23:25, 13 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 SRibonuclease S

RNase S is RNase A treated with subtilisin, which cleaves a single peptide bond. Consequently, Ribonuclease S consists of two fragments of bovine Ribonuclease A in a peptide-protein complex: S peptide (amino acids 1-20) and S protein (amino acids 21-124). RNase S was the third enzyme and fourth protein ever cystallized and three-dimensional structure determined. As such, biological work on RNase S helped scientists determine the first 3-dimensional structure of a protein-nucleic acid complex. Additionally, RNase S provided one of the first demonstrations of a crystalline enzyme acting as an active catalyst. Investigations of RNase S have also led to many technological advancements, including substrate leash amplification, fusion protein systems, and protein ubiquitination [1]. RNase S has been studied to reveal mechanisms of protein folding by coupling folding and association. Studies of RNase S has lead to greater interest in the investigation of RNase A and its role in biological systems, and has also lead to a greater knowledge of the correlation between protein folding and enzyme activity.


The image above depicts the surface interaction between the S peptide and S protein fragments; S peptide is blue, S protein is yellow.


RNase A and RNase S have very similar structures except for a few key areas, one being the cleavage site (residues 16-23)[1]. Decreased order in these amino acids is seen in RNase S. The on RNase A is located between residues Ala 20 and Ser 21. Upon cleavage, the fragments S peptide and S protein are created, giving RNase S its unique structure. consists of residues 1-20, and is largely responsible for proper folding. is comprised of residues 21-124. Additionally, RNase A and RNase S have many conserved structural components, as they are essentially the same protein. Glutamine 60 is highly conserved structurally between and , as well as in many different species, demonstrating its importance. Glu 60 is also interesting, because it is the only residue in an unfavorable position (Φ= -100, ψ= -130) as defined in the Ramachandran plot [2].



RNase S (PDB: 1RNU) is a protein composed of 2 fragments: S Peptide (residues 1-20) and S Protein (residues 21-124). It is a result of cleavage of RNase A between residues 20 and 21.

Drag the structure with the mouse to rotate


The of RNase S consists of His 12, Lys 41, Val 43, Asn 44, Thr 45, His 119, Phe 120, Asp 121, and Ser 123. is the only residue in the active site that is located on the S peptide fragment. are also crucial to the functioning of RNase S. Interestingly, both catalytic Histidines perform the same function, even though they are located on . Residues 1, 15-20, 21-23, and 124 could be removed without serious consequence to the structure or activity of RNase S. Residue 124 could also be removed from RNase A without compromising the structure. [3]


RNase A (PDB: 7rsa), also known as bovine pancreatic ribonuclease A, has been studied for years to learn about protein structure, stability, and folding.

Drag the structure with the mouse to rotate

















Hydrogen bonding and hydrophobic interactions play a major role in the structure of RNase S. [2] There are 84 water molecules present, with 8 of these specifically connecting S peptide and S protein. Some of these water molecules are also conserved throughout all RNase derivatives. Hydrophobic interactions between residues Phe 8, Met 13, His 12, Ala 4 are essential in holding the S Peptide in place. In addition to these residues, is also important in peptide-protein binding. In the picture, it appears that the protein and peptide are not connected; this is because the bond cleavage between residues 20 and 21 of RNase A has already occurred. Additionally RNase S has a rigid hydrophobic core; one-third of the surface of the core is made up of the S peptide. The surrounding loops have more flexibility.





References

"

  1. ↑ 1.0 1.1 Raines RT. Ribonuclease A. Chem Rev. 1998 May 7;98(3):1045-1066. PMID:11848924
  2. ↑ 2.0 2.1 Kim EE, Varadarajan R, Wyckoff HW, Richards FM. Refinement of the crystal structure of ribonuclease S. Comparison with and between the various ribonuclease A structures. Biochemistry. 1992 Dec 15;31(49):12304-14. PMID:1463719
  3. ↑ Wyckoff HW, Hardman KD, Allewell NM, Inagami T, Johnson LN, Richards FM. The structure of ribonuclease-S at 3.5 A resolution. J Biol Chem. 1967 Sep 10;242(17):3984-8. PMID:6037556

"

Other resources:

Wikipedia article on RNase A: http://en.wikipedia.org/wiki/Rnase_A

RNase S on PDB: http://www.rcsb.org/pdb/explore/explore.do?structureId=1RNU

RNase A on PDB: http://www.rcsb.org/pdb/explore/explore.do?structureId=7RSA

Ribonuclease on Proteopedia: http://proteopedia.org/wiki/index.php/Ribonuclease

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA, Melanie Clark, Ashton Chaffee, R. Jeremy Johnson
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