View source for 3cme

{{Large structure}}
==The Structure of CA and CCA-PHE-CAP-BIO Bound to the Large Ribosomal Subunit of Haloarcula Marismortui==
<StructureSection load='3cme' size='340' side='right' caption='[[3cme]], [[Resolution|resolution]] 2.95&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3cme]] is a 32 chain structure with sequence from [http://en.wikipedia.org/wiki/Haloarcula_marismortui Haloarcula marismortui]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CME OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3CME FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACA:6-AMINOHEXANOIC+ACID'>ACA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PHE:PHENYLALANINE'>PHE</scene>, <scene name='pdbligand=SR:STRONTIUM+ION'>SR</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=1MA:6-HYDRO-1-METHYLADENOSINE-5-MONOPHOSPHATE'>1MA</scene>, <scene name='pdbligand=8AN:3-AMINO-3-DEOXYADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>8AN</scene>, <scene name='pdbligand=OMG:O2-METHYLGUANOSINE-5-MONOPHOSPHATE'>OMG</scene>, <scene name='pdbligand=OMU:O2-METHYLURIDINE+5-MONOPHOSPHATE'>OMU</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene>, <scene name='pdbligand=UR3:3-METHYLURIDINE-5-MONOPHOSHATE'>UR3</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3cma|3cma]]</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3cme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cme OCA], [http://pdbe.org/3cme PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3cme RCSB], [http://www.ebi.ac.uk/pdbsum/3cme PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3cme ProSAT]</span></td></tr>
</table>
{{Large structure}}
== Function ==
[[http://www.uniprot.org/uniprot/RL24E_HALMA RL24E_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00773] [[http://www.uniprot.org/uniprot/RLA0_HALMA RLA0_HALMA]] Ribosomal protein L10e is the functional equivalent of E.coli protein L10.[HAMAP-Rule:MF_00280] [[http://www.uniprot.org/uniprot/RL21_HALMA RL21_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_00369] [[http://www.uniprot.org/uniprot/RL3_HALMA RL3_HALMA]] One of the primary rRNA binding proteins, it binds directly near the 3'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01325_A] [[http://www.uniprot.org/uniprot/RL2_HALMA RL2_HALMA]] One of the primary rRNA binding proteins. Required for association of the 30S and 50S subunits to form the 70S ribosome, for tRNA binding and peptide bond formation. It has been suggested to have peptidyltransferase activity; this is somewhat controversial. Makes several contacts with the 16S rRNA in the 70S ribosome (By similarity).[HAMAP-Rule:MF_01320_A] [[http://www.uniprot.org/uniprot/RL22_HALMA RL22_HALMA]] This protein binds specifically to 23S rRNA. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331]  Contacts all 6 domains of the 23S rRNA, helping stabilize their relative orientation. An extended beta-hairpin in the C-terminus forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L4, while most of the rest of the protein is located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01331] [[http://www.uniprot.org/uniprot/RL19E_HALMA RL19E_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01475] [[http://www.uniprot.org/uniprot/RL37_HALMA RL37_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00547] [[http://www.uniprot.org/uniprot/RL32_HALMA RL32_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_00810] [[http://www.uniprot.org/uniprot/RL39_HALMA RL39_HALMA]] Binds to the 23S rRNA. Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_00629] [[http://www.uniprot.org/uniprot/RL24_HALMA RL24_HALMA]] One of two assembly initiator proteins, it binds directly to the 5'-end of the 23S rRNA, where it nucleates assembly of the 50S subunit (By similarity).[HAMAP-Rule:MF_01326_A]  Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_A] [[http://www.uniprot.org/uniprot/RL18_HALMA RL18_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, where it forms part of the central protuberance and stabilizes the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01337_A] [[http://www.uniprot.org/uniprot/RL31_HALMA RL31_HALMA]] Binds to the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00410] [[http://www.uniprot.org/uniprot/RL13_HALMA RL13_HALMA]] This protein is one of the early assembly proteins of the 50S ribosomal subunit (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL14_HALMA RL14_HALMA]] Forms part of two intersubunit bridges in the 70S ribosome (By similarity). Binds to 23S rRNA.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RL29_HALMA RL29_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain I) to which it binds. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RL30_HALMA RL30_HALMA]] This is one of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains.[HAMAP-Rule:MF_01371] [[http://www.uniprot.org/uniprot/RL44E_HALMA RL44E_HALMA]] Binds to the 23S rRNA. Binds deacetylated tRNA in the E site; when the tRNA binds a stretch of 7 amino acids are displaced to allow binding.[HAMAP-Rule:MF_01476] [[http://www.uniprot.org/uniprot/RL7A_HALMA RL7A_HALMA]] Multifunctional RNA-binding protein that recognizes the K-turn motif in ribosomal RNA, box H/ACA and box C/D sRNAs (By similarity).[HAMAP-Rule:MF_00326] [[http://www.uniprot.org/uniprot/RL4_HALMA RL4_HALMA]] One of the primary rRNA binding proteins, this protein initially binds near the 5'-end of the 23S rRNA. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01328_A]  Makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit.[HAMAP-Rule:MF_01328_A]  Forms part of the polypeptide exit tunnel, in which it helps forms a bend with protein L22. Contacts the macrolide antibiotic spiramycin in the polypeptide exit tunnel.[HAMAP-Rule:MF_01328_A] [[http://www.uniprot.org/uniprot/RL11_HALMA RL11_HALMA]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_00736_A] [[http://www.uniprot.org/uniprot/RL15_HALMA RL15_HALMA]] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341_A] [[http://www.uniprot.org/uniprot/RL18E_HALMA RL18E_HALMA]] Stabilizes the tertiary rRNA structure within the 23S rRNA domain (domain II) to which it binds.[HAMAP-Rule:MF_00329] [[http://www.uniprot.org/uniprot/RL10_HALMA RL10_HALMA]] This is 1 of 5 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Modeling places the A and P site tRNAs in close proximity to this protein.[HAMAP-Rule:MF_00448] [[http://www.uniprot.org/uniprot/RL5_HALMA RL5_HALMA]] This is 1 of 5 proteins that mediates the attachment of the 5S rRNA onto the large ribosomal subunit, stabilizing the orientation of adjacent RNA domains. Forms part of the central protuberance. Modeling places the A and P site tRNAs in close proximity to this protein; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs. In the 70S ribosome it is thought to contact protein S13 of the 30S subunit (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement.[HAMAP-Rule:MF_01333_A] [[http://www.uniprot.org/uniprot/RL23_HALMA RL23_HALMA]] Binds to a specific region on the 23S rRNA. Located at the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL6_HALMA RL6_HALMA]] This protein binds to the 23S rRNA, and is important in its secondary structure. It is located near the subunit interface in the base of the L7/L12 stalk, and near the tRNA binding site of the peptidyltransferase center.[HAMAP-Rule:MF_01365] 
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cm/3cme_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=3cme ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The last step in ribosome-catalyzed protein synthesis is the hydrolytic release of the newly formed polypeptide from the P-site bound tRNA. Hydrolysis of the ester link of the peptidyl-tRNA is stimulated normally by the binding of release factors (RFs). However, an unacylated tRNA or just CCA binding to the ribosomal A site can also stimulate deacylation under some nonphysiological conditions. Although the sequence of events is well described by biochemical studies, the structural basis of the mechanism underlying this process is not well understood. Two new structures of the large ribosomal subunit of Haloarcula marismortui complexed with a peptidyl-tRNA analog in the P site and two oligonucleotide mimics of unacylated tRNA, CCA and CA, in the A site show that the binding of either CA or CCA induces a very similar conformational change in the peptidyl-transferase center as induced by aminoacyl-CCA. However, only CCA positions a water molecule appropriately to attack the carbonyl carbon of the peptidyl-tRNA and stabilizes the proper orientation of the ester link for hydrolysis. We, thus, conclude that both the ability of the O3'-hydroxyl group of the A-site A76 to position the water and the A-site CCA induced conformational change of the PTC are critical for the catalysis of the deacylation of the peptidyl-tRNA by CCA, and perhaps, an analogous mechanism is used by RFs.

Peptidyl-CCA deacylation on the ribosome promoted by induced fit and the O3'-hydroxyl group of A76 of the unacylated A-site tRNA.,Simonovic M, Steitz TA RNA. 2008 Nov;14(11):2372-8. Epub 2008 Sep 25. PMID:18818369<ref>PMID:18818369</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 3cme" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Haloarcula marismortui]]
[[Category: Simonovic, M]]
[[Category: Steitz, T A]]
[[Category: Hydrolysis of peptidyl-trna]]
[[Category: Protein-protein complex]]
[[Category: Protein-rna complex]]
[[Category: Ribosome]]
[[Category: Ribosome 50]]
[[Category: Rna-rna complex]]