User:Wayne Decatur/Haloarcula Large Ribosomal Subunit: Difference between revisions
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m addec clarification about not all of RNA bases being represented |
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::*It is important to note that '''the ribosome is highly conserved, particularly the nucleotides close to the Yarus analog in Domain V and thus the major conclusions reached from the structure are applicable to all ribosomes'''. | ::*It is important to note that '''the ribosome is highly conserved, particularly the nucleotides close to the Yarus analog in Domain V and thus the major conclusions reached from the structure are applicable to all ribosomes'''. | ||
:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozyme/13'>No proteins approach close enough to the active site to affect the chemistry of peptide bond synthesis</scene> | :<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozyme/13'>No proteins approach close enough to the active site to affect the chemistry of peptide bond synthesis</scene> | ||
:*<font color="dodgerblue">'''L2'''</font>, <font color="lightblue">'''L3'''</font>, <font color="#ae00fe">'''L4'''</font> and <font color="darkgreen">'''L10e'''</font> are the nearest proteins to the <font color="magenta">'''Yarus analog'''</font> bound to <font color="red">'''domain V'''</font> of the subunit. Note that it may help to start from | :*<font color="dodgerblue">'''L2'''</font>, <font color="lightblue">'''L3'''</font>, <font color="#ae00fe">'''L4'''</font> and <font color="darkgreen">'''L10e'''</font> are the nearest proteins to the <font color="magenta">'''Yarus analog'''</font> bound to <font color="red">'''domain V'''</font> of the subunit. Note that it may help to start from <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststartplusanalog/1'> the entire subunit with analog bound</scene> before hitting the above <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozyme/13'>scene link</scene> to get a good sense of these elements in the core of the subunit or use <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewall/3'>this scene with the rest of the subunit shown translucently</scene>. With <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewp/2'>all the proteins shown it is obvious these four proteins are the closest.</scene> | ||
:*Examining the distance of the proteins from the '''phosphorous analog of the tetrahedral carbon''' (<font color="yellow">'''in yellow'''</font>) indicates none of the proteins are close enough to be involved in the chemistry of peptide bond synthesis. '''Even the closest protein is over 15 Å away'''.<small>(In the eubacterial ribosomes , e.g., [[2j01]],[[2i2v]], and [[2wdn]], the N-terminus of a non-universally conserved protein, L27, also comes close to the active site<ref>PMID: 16285924</ref><ref>PMID: 18393533</ref><ref>PMID: 19363482</ref>.)</small> | :*Examining the distance of the proteins from the '''phosphorous analog of the tetrahedral carbon''' (<font color="yellow">'''in yellow'''</font>) indicates none of the proteins are close enough to be involved in the chemistry of peptide bond synthesis. '''Even the closest protein is over 15 Å away'''.<small>(In the eubacterial ribosomes , e.g., [[2j01]],[[2i2v]], and [[2wdn]], the N-terminus of a non-universally conserved protein, L27, also comes close to the active site<ref>PMID: 16285924</ref><ref>PMID: 18393533</ref><ref>PMID: 19363482</ref>.)</small> | ||
:*As touched on earlier in this section as well as [[#The rRNA domains:|in an earlier section]], it is in fact, <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewprna/2'>the RNA of Domain V that is intimately associated with the active site of the ribosome</scene>, leaving little doubt that the ribosome is indeed a ribozyme. | :*As touched on earlier in this section as well as [[#The rRNA domains:|in an earlier section]], it is in fact, <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewprna/2'>the RNA of Domain V that is intimately associated with the active site of the ribosome</scene>, leaving little doubt that the ribosome is indeed a ribozyme. | ||
::*<small>Keep in mind that in order to make this lare molecule load in reasonable times over the internet, the RNA has been simplified by leaving out the information for most of the bases and in fact if all the bases were included it would look even more crowded with RNA at the active site.</small> | ::*<small>Keep in mind that in order to make this lare molecule load in reasonable times over the internet, the RNA has been simplified by leaving out the information for most of the bases and in fact if all the bases were included it would look even more crowded with RNA at the active site.</small> | ||
:'''SUMMARY: Only RNA is in proximity to the site of peptide bond synthesis, and therefore the chemistry of peptide bond synthesis is not catalyzed by protein and in fact the ribosome is a ribozyme with the peptidyl transferase reaction being catalyzed by RNA'''. | :'''SUMMARY: Only RNA is in proximity to the site of peptide bond synthesis, and therefore the chemistry of peptide bond synthesis is not catalyzed by protein and in fact the ribosome is a ribozyme with the peptidyl transferase reaction being catalyzed by RNA'''. | ||
===Polypeptide Exit Tunnel:=== | ===Polypeptide Exit Tunnel:=== | ||
