View source for 1vy5

==Crystal structure of the Thermus thermophilus 70S ribosome in the post-catalysis state of peptide bond formation containing dipeptydil-tRNA in the A site and deacylated tRNA in the P site.==
<StructureSection load='1vy5' size='340' side='right' caption='[[1vy5]], [[Resolution|resolution]] 2.55&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1vy5]] is a 112 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. This structure supersedes and combines the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcq 4qcq], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcr 4qcr], [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qcs 4qcs] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=4qct 4qct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VY5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1VY5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=K:POTASSIUM+ION'>K</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=31M:3-DEOXY-3-[(L-METHIONYL-L-PHENYLALANYL)AMINO]ADENOSINE+5-(DIHYDROGEN+PHOSPHATE)'>31M</scene>, <scene name='pdbligand=4SU:4-THIOURIDINE-5-MONOPHOSPHATE'>4SU</scene>, <scene name='pdbligand=5MC:5-METHYLCYTIDINE-5-MONOPHOSPHATE'>5MC</scene>, <scene name='pdbligand=5MU:5-METHYLURIDINE+5-MONOPHOSPHATE'>5MU</scene>, <scene name='pdbligand=7MG:7N-METHYL-8-HYDROGUANOSINE-5-MONOPHOSPHATE'>7MG</scene>, <scene name='pdbligand=MIA:2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5-MONOPHOSPHATE'>MIA</scene>, <scene name='pdbligand=PSU:PSEUDOURIDINE-5-MONOPHOSPHATE'>PSU</scene></td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4qcq|4qcq]], [[4qcr|4qcr]], [[4qcs|4qcs]], [[4qct|4qct]]</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=1vy5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vy5 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1vy5 RCSB], [http://www.ebi.ac.uk/pdbsum/1vy5 PDBsum]</span></td></tr>
</table>
{{Large structure}}
== Function ==
[[http://www.uniprot.org/uniprot/RL9_THET8 RL9_THET8]] Binds to the 23S rRNA. Extends more that 50 Angstroms beyond the surface of the 70S ribosome.[HAMAP-Rule:MF_00503] [[http://www.uniprot.org/uniprot/RL6_THET8 RL6_THET8]] 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] [[http://www.uniprot.org/uniprot/RSHX_THET8 RSHX_THET8]] Binds at the top of the head of the 30S subunit. It stabilizes a number of different RNA elements and thus is important for subunit structure. [[http://www.uniprot.org/uniprot/RS7_THET8 RS7_THET8]] One of the primary rRNA binding proteins, it binds directly to 3'-end of the 16S rRNA where it nucleates assembly of the head domain of the 30S subunit. Is located at the subunit interface close to the decoding center. Binds mRNA and the E site tRNA blocking its exit path in the ribosome. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_00480_B] [[http://www.uniprot.org/uniprot/RS2_THET8 RS2_THET8]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [[http://www.uniprot.org/uniprot/RS17_THET8 RS17_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform and body of the 30S subunit by bringing together and stabilizing interactions between several different RNA helices. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01345]  Deletion of the protein leads to an increased generation time and a temperature-sensitive phenotype.[HAMAP-Rule:MF_01345] [[http://www.uniprot.org/uniprot/RS18_THET8 RS18_THET8]] Located on the back of the platform of the 30S subunit where it stabilizes the close packing of several RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it probably interacts with the Shine-Dalgarno helix.[HAMAP-Rule:MF_00270] [[http://www.uniprot.org/uniprot/RL4_THET8 RL4_THET8]] 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. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01328_B]  Forms part of the polypeptide exit tunnel (By similarity).[HAMAP-Rule:MF_01328_B]  This protein can be incorporated into E.coli ribosomes in vivo, which resulted in decreased peptidyltransferase (Ptase) activity of the hybrid ribosomes. The hybrid 50S subunits associate less well with 30S subunits to form the ribosome.[HAMAP-Rule:MF_01328_B] [[http://www.uniprot.org/uniprot/RS16_THET8 RS16_THET8]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains.[HAMAP-Rule:MF_00385] [[http://www.uniprot.org/uniprot/RL23_THET8 RL23_THET8]] One of the early assembly proteins (By similarity) it binds 23S rRNA. One of the proteins that surrounds the polypeptide exit tunnel on the outside of the ribosome. Forms the main docking site for trigger factor binding to the ribosome (By similarity).[HAMAP-Rule:MF_01369] [[http://www.uniprot.org/uniprot/RL2_THET8 RL2_THET8]] 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 (By similarity). Makes several contacts with the 16S rRNA (forming bridge B7b) in the 70S ribosome.[HAMAP-Rule:MF_01320_B] [[http://www.uniprot.org/uniprot/RL19_THET8 RL19_THET8]] Contacts the 16S rRNA of the 30S subunit (part of bridge B6), connecting the 2 subunits.[HAMAP-Rule:MF_00402] [[http://www.uniprot.org/uniprot/RS14Z_THET8 RS14Z_THET8]] Required for the assembly of 30S particles and may also be responsible for determining the conformation of the 16S rRNA at the A site (By similarity). Binds 16S rRNA in center of the 30S subunit head.[HAMAP-Rule:MF_01364_B] [[http://www.uniprot.org/uniprot/RS20_THET8 RS20_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the bottom of the body of the 30S subunit, by binding to several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00500] [[http://www.uniprot.org/uniprot/RL29_THET8 RL29_THET8]] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [[http://www.uniprot.org/uniprot/RS10_THET8 RS10_THET8]] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [[http://www.uniprot.org/uniprot/RL5_THET8 RL5_THET8]] This is 1 of the proteins that binds and probably mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance. In the 70S ribosome it contacts protein S13 of the 30S subunit (forming bridge B1b) connecting the head of the 30S subunit to the top of the 50S subunit. The bridge itself contacts the P site tRNA and is implicated in movement during ribosome translocation. Also contacts the P site tRNA independently of the intersubunit bridge; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RL14_THET8 RL14_THET8]] This protein binds directly to 23S ribosomal RNA (By similarity).[HAMAP-Rule:MF_01367]  Contacts the 16S rRNA of the 30S subunit in two different positions helping to form bridges B5 and B8.[HAMAP-Rule:MF_01367] [[http://www.uniprot.org/uniprot/RS11_THET8 RS11_THET8]] Located on the upper part of the platform of the 30S subunit, where it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome, where it interacts both with the Shine-Dalgarno helix and mRNA.[HAMAP-Rule:MF_01310] [[http://www.uniprot.org/uniprot/RL33_THET8 RL33_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00294]  Contacts the E site tRNA.[HAMAP-Rule:MF_00294] [[http://www.uniprot.org/uniprot/RL21_THET8 RL21_THET8]] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). Found on the solvent side of the large subunit.[HAMAP-Rule:MF_01363] [[http://www.uniprot.org/uniprot/RL25_THET8 RL25_THET8]] This is one of 3 proteins that mediate the attachment of the 5S rRNA onto the large ribosomal subunit.[HAMAP-Rule:MF_01334] [[http://www.uniprot.org/uniprot/RS13_THET8 RS13_THET8]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome structure it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the top of the two subunits; these bridges are in contact with the A site and P site tRNAs respectively and are implicated in movement during ribosome translocation. Separately contacts the tRNAs in the A and P sites.[HAMAP-Rule:MF_01315] [[http://www.uniprot.org/uniprot/RL3_THET8 RL3_THET8]] 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_B] [[http://www.uniprot.org/uniprot/RS6_THET8 RS6_THET8]] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [[http://www.uniprot.org/uniprot/RL18_THET8 RL18_THET8]] This is one of the proteins that binds and mediates the attachment of the 5S RNA into the large ribosomal subunit, where it forms part of the central protuberance.[HAMAP-Rule:MF_01337_B] [[http://www.uniprot.org/uniprot/RS3_THET8 RS3_THET8]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01309_B] [[http://www.uniprot.org/uniprot/RL15_THET8 RL15_THET8]] Binds to the 23S rRNA (By similarity).[HAMAP-Rule:MF_01341_B] [[http://www.uniprot.org/uniprot/RS9_THET8 RS9_THET8]] Part of the top of the head of the 30S subunit. The C-terminal region penetrates the head emerging in the P-site where it contacts tRNA.[HAMAP-Rule:MF_00532_B] [[http://www.uniprot.org/uniprot/RL31_THET8 RL31_THET8]] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501] [[http://www.uniprot.org/uniprot/RL20_THET8 RL20_THET8]] Binds directly to 23S ribosomal RNA and is necessary for the in vitro assembly process of the 50S ribosomal subunit. It is not involved in the protein synthesizing functions of that subunit (By similarity).[HAMAP-Rule:MF_00382] [[http://www.uniprot.org/uniprot/RS12_THET8 RS12_THET8]] With S4 and S5 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_00403_B]  Interacts with and stabilizes bases of the 16S rRNA that are involved in tRNA selection in the A site and with the mRNA backbone. Located at the interface of the 30S and 50S subunits, it traverses the body of the 30S subunit contacting proteins on the other side and probably holding the rRNA structure together. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_00403_B] [[http://www.uniprot.org/uniprot/RL27_THET8 RL27_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00539] [[http://www.uniprot.org/uniprot/RS15_THET8 RS15_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit by binding and bridging several RNA helices of the 16S rRNA (By similarity).[HAMAP-Rule:MF_01343]  Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome.[HAMAP-Rule:MF_01343] [[http://www.uniprot.org/uniprot/RS8_THET8 RS8_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the platform of the 30S subunit central domain. The combined cluster of proteins S8, S12 and S17 appears to hold together the shoulder and platform of the 30S subunit.[HAMAP-Rule:MF_01302_B] [[http://www.uniprot.org/uniprot/RL32_THET8 RL32_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00340] [[http://www.uniprot.org/uniprot/RS4_THET8 RS4_THET8]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it helps nucleate assembly of the body and platform of the 30S subunit. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01306_B] [[http://www.uniprot.org/uniprot/RL13_THET8 RL13_THET8]] This protein is one of the early assembly proteins of the 50S ribosomal subunit, although it is not seen to bind rRNA by itself. It is important during the early stages of 50S assembly (By similarity).[HAMAP-Rule:MF_01366] [[http://www.uniprot.org/uniprot/RL24_THET8 RL24_THET8]] 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_B]  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_01326_B] [[http://www.uniprot.org/uniprot/RL16_THET8 RL16_THET8]] This protein binds directly to 23S rRNA. Interacts with the A site tRNA.[HAMAP-Rule:MF_01342] [[http://www.uniprot.org/uniprot/RL22_THET8 RL22_THET8]] This protein binds specifically to 23S rRNA; its binding is stimulated by other ribosomal proteins, e.g. L4, L17, and L20. It is important during the early stages of 50S assembly. It makes multiple contacts with different domains of the 23S rRNA in the assembled 50S subunit and ribosome (By similarity).[HAMAP-Rule:MF_01331_B]  The globular domain of the protein is one of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that penetrates into the center of the 70S ribosome. This extension seems to form part of the wall of the exit tunnel.[HAMAP-Rule:MF_01331_B] [[http://www.uniprot.org/uniprot/RS19_THET8 RS19_THET8]] Located at the top of the head of the 30S subunit, extending towards the 50S subunit, which it may contact in the 70S complex. Contacts several RNA helices of the 16S rRNA.[HAMAP-Rule:MF_00531] [[http://www.uniprot.org/uniprot/RL34_THET8 RL34_THET8]] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00391] [[http://www.uniprot.org/uniprot/RS5_THET8 RS5_THET8]] With S4 and S12 plays an important role in translational accuracy (By similarity).[HAMAP-Rule:MF_01307_B]  Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. Binds mRNA in the 70S ribosome, positioning it for translation.[HAMAP-Rule:MF_01307_B] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
During peptide-bond formation on the ribosome, the alpha-amine of an aminoacyl-tRNA attacks the ester carbonyl carbon of a peptidyl-tRNA to yield a peptide lengthened by one amino acid. Although the ribosome's contribution to catalysis is predominantly entropic, the lack of high-resolution structural data for the complete active site in complex with full-length ligands has made it difficult to assess how the ribosome might influence the pathway of the reaction. Here, we present crystal structures of preattack and postcatalysis complexes of the Thermus thermophilus 70S ribosome at ~2.6-A resolution. These structures reveal a network of hydrogen bonds along which proton transfer could take place to ensure the concerted, rate-limiting formation of a tetrahedral intermediate. We propose that, unlike earlier models, the ribosome and the A-site tRNA facilitate the deprotonation of the nucleophile through the activation of a water molecule.

A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome.,Polikanov YS, Steitz TA, Innis CA Nat Struct Mol Biol. 2014 Aug 17. doi: 10.1038/nsmb.2871. PMID:25132179<ref>PMID:25132179</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Thermus thermophilus]]
[[Category: Innis, C A]]
[[Category: Polikanov, Y S]]
[[Category: Steitz, T A]]
[[Category: Acylated trna]]
[[Category: Peptydil transfer reaction]]
[[Category: Proton transfer mechanism]]
[[Category: Ribosome]]
[[Category: Translation]]