User:Wayne Decatur/Haloarcula Large Ribosomal Subunit: Difference between revisions

The [[ribosome]] is a complex composed of RNA and protein that adds up to several million daltons in size and plays a critical role in the process of decoding the genetic information stored in the genome into protein as outlined in what is now known as the Central Dogma of Molecular Biology<ref>[http://sandwalk.blogspot.com/2009/10/ribosome-and-central-dogma-of-molecular.html the Central Dogma of Molecular Biology clarified]</ref>. Specifically, the ribosome carries out the process of translation, decoding the genetic information encoded in messenger RNA, one amino acid at a time, into newly synthesized polypeptide chains. The ribosome functions as a complex of two complexes of many proteins and RNAs of substantial length; these two complexes are the small ribosomal subunit and the large ribosomal subunit. The formation of peptide bonds occurs in the large subunit where the acceptor-stems of the tRNAs are docked.  

For this landmark structure, Thomas A. Steitz of Yale University shared [[Nobel Prizes for 3D Molecular Structure#Twenty-First Century|the 2009 Nobel Prize in Chemistry]]<ref>[http://nobelprize.org/nobel_prizes/chemistry/laureates/2009/ The Nobel Prize in Chemistry 2009 page at The Official Web Site of the Nobel Prize]</ref><ref>PMID: 20509130</ref> along with two other structural biologists working on the ribosome. It is important to note that the Steitz lab worked with the Moore lab on this phenomenal accomplishment although the Nobel committee limits the award itself to up to three laureates.  

The large subunit of the <em>Haloracula marismortui</em> ribosome sediments at 50S, as do the large subunits of archaea and eubacteria. It is composed of two chains of RNA, a 23S chain (2,922 nucleotides long, 946 kDa) and a 5S chain (122 bases long, 39 kDa). Assembled with the RNA are 27 protein chains (of a total of 31 known), varying in length from 49 (L39E, 6 kDa) to 337 amino acids (L3, 37 kDa)<ref>PMID:10937989</ref>.

:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72monolith/1'>The solved large subunit is a monolith</scene>.

:*It is important to note that two stalks (the L1 stalk and L7/L12 stalk) seen in lower resolution structures on each side of the large ribosomal subunit at lower resolution<ref>PMID: 9657144</ref> are not visible in the higher resolution structure viewed here. Thus, ''in actuality'' the Haloarcula large subunit has a less monolithic appearance with other protuberances on either side of the central one, yet clearly not possessing the distinct domains formed by the distinct rRNA domains visible in the secondary structure (see below).

:#a small <font color="magenta">'''5S rRNA'''</font> (122 nucleotides)which forms part of the central protuberance seen in the large subunit.

:#a large <font color="#fd0162">'''23S rRNA'''</font> (3045 nucleotides) - 2833 of the 3045 nucleotides of the <font color="#fd0162">23S rRNA</font> are seen in the structure.

The secondary structure map of Haloarcula 23S rRNA (below) clearly shows six large RNA domains extending off a large major loop.<br>

:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomains/3'>The six domains of the large subunit ribosomal RNA and 5S rRNA fit into the monolithic subunit like puzzle pieces</scene>:

:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72beststartdomain1/3'>Domain I</scene> (<font color = "#6080ff">'''shown in blue'''</font>)

:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain2/5'>Domain II</scene> (<font color = "cyan">'''shown in cyan'''</font>)

:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain3/6'>Domain III</scene> (<font color = "yellow">'''shown in yellow'''</font>)

:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain4/7'>Domain IV</scene> (<font color = "#00FF00">'''shown in green'''</font>)

::*<small>Helix 69 is a portion of Domain IV <ref>Helix 69 is shown clearly in Domain IV in [http://people.biochem.umass.edu/fournierlab/3dmodmap/hmarlsu2dframes.php a detailed secondary structure of Haloarcula marismortui 23S rRNA]</ref>and is part of one of the important conserved intersubunit bridges of the ribosome (b2a), although '''it is not visible in this structure'''. (The 13-nt stem-loop not seen would connect the highlighted spheres <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain4h69/2'>here</scene>.) See the [[ribosome]] to see a structure where helix 69 is observed in the solved structure, extending from the large subunit under the A- and P- site tRNAs in the 70S ribosome and contacting the tRNAs and the small subunit decoding center. Helix 69 plays a roles in initiation, termination, and disassembly of the ribosome post-termination</small><ref>PMID: 17996252</ref><ref>PMID: 19007789</ref><ref>PMID: 16973438</ref>.

:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain5/6'>Domain V</scene> (<font color = "red">'''shown in red'''</font>)

::*<font color="red">'''Domain V'''</font> lies at the core of the subunit. &nbsp; It is known to be intimately associated with the peptidyl transferase reaction that occurs during translation. This is further explored further [[#The ribosome is a ribozyme - protein DOES NOT participate directly in the chemistry of peptide bond synthesis:|below]].

:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain6/6'>Domain VI</scene> (<font color = "#ae00fe">'''shown in purple'''</font>)

:*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s725srrns/3'>5S rRNA</scene> (<font color = "#FF00FF">'''shown in magenta'''</font>), though a separate molecule, is effectively the seventh RNA domain of the large subunit.

:*Proteins are generally globular.  However, while about half the 27 proteins seen in the crystal structure of the large ribosomal subunit are globular (<font color="orange">'''shown as orange'''</font>), interestingly, '''the other half are extended or have large extended regions''' emanating from globular domains (<font color="cyan">'''shown as cyan'''</font>).   

:*For contrast, the globular L7ae is shown. The extended regions are <font color="cyan">'''highlighted in cyan'''</font>.   

:*View of L2, L15, L39e and L7ae again but with the RNA backbone shown. The extended regions are <font color="cyan">'''again highlighted in cyan'''</font>.   

:*This view is also a good point to note the fact that the ribosomal proteins do not encase the nucleic acid as with [[Human Immunodeficiency Virus|spherical viruses]] or with [[1vtm|Tobacco mosaic virus]], nor do the proteins become surrounded by the nucleic acid as in the [[Nucleosomes|nucleosome]].  

:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain5allwithyarus/9'>An informative analog is observed at the core of the large subunit bound to Domain V</scene> (<font color = "red">'''shown in red'''</font>)

:*In addition to unliganded subunit, the large subunit structure has been solved with substrate analogs which provides a detailed view of the direct role <font color="red">'''domain V'''</font> plays in the chemistry of peptide bond synthesis.  One of the analogs was the <font color="magenta">'''Yarus analog (CCA-puromycin)'''</font>, known to inhibit translation because it mimics normal substrate, specifically it resembles an unstable transition state intermediate formed during peptide bond synthesis and involving the extreme ends of the A- and P- tRNAs and atoms corresponding to parts of an amino acid. <scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain5withyarus/4'>The Yarus analog (magenta), indicating the site of the petidyl transferase reaction, is entrenched in Domain V</scene>.

::*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72rrnadomain5withyarusnts/5'>Guanosine 2284 (orange) and Guanosine 2285 (blue) are base-paired</scene> with the <font color="magenta">'''Yarus analog'''</font>.

::*<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s722486yarus/1'>One atom in particular corresponds to the carbon of the tetrahedral carbon intermediate of the peptidyl transferase reaction</scene><ref>PMID: 10937990</ref>, and <font color = "red">'''A2486'''</font> (E. coli #2451) of <font color = "red">'''Domain V'''</font> approaches this critical atom of the <font color="magenta">'''Yarus analog'''</font>. The individual components of the <font color="magenta">'''Yarus analog'''</font> are labeled.

:*<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>

:*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.

:<scene name='User:Wayne_Decatur/Sandbox_Haloarcula_Ribosomal_Large_Subunit/1s72tunnelend/2'>The end of the Polypeptide Exit Tunnel is shown in the center</scene>

:*As the nascent chain grows, it advances into <font color="dodgerblue">'''a tunnel'''</font> about 100 angstroms long that passes through the large subunit, called the polypeptide exit tunnel.

 

:*A number of antibiotics, including the [[User:Wayne Decatur/Haloarcula Large Ribosomal Subunit With Azithromycin|macrolide Azithromycin (zithromax)]], binds to this region of the tunnel.

<b>Steitz and Moore labs original atomic-resolution structures</b><ref>PMID:10937989</ref><ref>PMID: 10937990</ref>: <em>Haloarcula marismortui</em> large ribosomal subunit - [[1ffk]] and later refined to give [[1jj2]]<ref>PMID:11483524</ref>, and then refined to give [[1s72]]<ref>PMID:15184028</ref>, [[2qa4]]<ref>PMID:17599351</ref>, and later [[3cc2]]<ref>PMID:18455733</ref>. Related: [[1ffz]], [[1fg0]].  Assembled with the ribosomal RNAs (2,922 and 122 nucleotides long) in the structure are 27 protein chains (of a total of 31 known), varying in length from 49 (L39E, 6 kDa) to 337 amino acids (L3, 37 kDa).<ref>PMID:10937989</ref>

* [[Highest impact structures]] of all time

==References and Notes==

==Additional Literature==

<ref group="xtra">PMID:19222865</ref><ref group="xtra">PMID: 18292779</ref><ref group="xtra">PMID: 19962317</ref><ref group="xtra">PMID: 19838167</ref><ref group="xtra">PMID: 11297922</ref><ref group="xtra">PMID: 20562215</ref><ref group="xtra">PMID: 23771137</ref><references group="xtra"/>