User:Wayne Decatur/Haloarcula Large Ribosomal Subunit: Difference between revisions
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:*The globular domains are the portions of the proteins on the subunit's exterior, nestling in the gaps and crevices of the folded RNA. You may need to use the mouse to move the structure around to convince yourself. | :*The globular domains are the portions of the proteins on the subunit's exterior, nestling in the gaps and crevices of the folded RNA. You may need to use the mouse to move the structure around to convince yourself. | ||
:*This view is also a good point to note the fact that the ribosomal proteins do not encase the nucleic acid as with [http://en.wikipedia.org/wiki/Virus spherical viruses or with Tobacco mosaic virus], nor do the proteins become surrounded by the nucleic acid as in the [[Nucleosomes|nucleosome]]. | :*This view is also a good point to note the fact that the ribosomal proteins do not encase the nucleic acid as with [http://en.wikipedia.org/wiki/Virus spherical viruses or with Tobacco mosaic virus], nor do the proteins become surrounded by the nucleic acid as in the [[Nucleosomes|nucleosome]]. | ||
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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/12'>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/12'>No proteins approach close enough to the active site to affect the chemistry of peptide bond synthesis</scene> | ||
:*<font color="yellow">'''L2'''</font>, <font color="lightblue">'''L3'''</font>, <font color="#ae00fe">'''L4'''</font> and <font color="#228b22">'''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 you may wish to start from the <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3'>initial scene</scene> before hitting the above <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozyme/12'>scene link</scene> to better visualize the location of these elements in the core of the subunit. | :*<font color="yellow">'''L2'''</font>, <font color="lightblue">'''L3'''</font>, <font color="#ae00fe">'''L4'''</font> and <font color="#228b22">'''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 you may wish to start from the <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststart/3'>initial scene</scene> before hitting the above <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozyme/12'>scene link</scene> to better visualize the location of these elements in the core of the subunit or use <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewall/2'>this scene with the rest of the large subunit transparent</scene>. With <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72ribozymewp/1'>all the proteins shown you can easily convince yourself these are the four 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 | :*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 [[#The rRNA domains:|in an earlier section]], it is in fact, <font color="#fd0162">RNA</font> that is intimately associated with the active site of the ribosome, leaving little doubt that the ribosome is indeed a ribozyme. | :*As touched on [[#The rRNA domains:|in an earlier section]], it is in fact, <font color="#fd0162">RNA</font> that is intimately associated with the active site of the ribosome, leaving little doubt that the ribosome is indeed a ribozyme. | ||
:'''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'''. | ||
