View source for 6c5l


==Conformation of methylated GGQ in the Peptidyl Transferase Center during translation termination (T. thermophilus)==
<StructureSection load='6c5l' size='340' side='right'caption='[[6c5l]], [[Resolution|resolution]] 3.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[6c5l]] is a 118 chain structure with sequence from [http://en.wikipedia.org/wiki/ ], [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971] and [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C5L OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C5L FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=MEQ:N5-METHYLGLUTAMINE'>MEQ</scene>, <scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">prfB, Ththe16_0244 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 "Flavobacterium thermophilum" Yoshida and Oshima 1971])</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=6c5l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c5l OCA], [http://pdbe.org/6c5l PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c5l RCSB], [http://www.ebi.ac.uk/pdbsum/6c5l PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c5l ProSAT]</span></td></tr>
</table>
== Function ==
[[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/RSHX_THETH RSHX_THETH]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RS7_THET2 RS7_THET2]] One of the primary rRNA binding proteins, it binds directly to 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, probably blocks exit of the E-site tRNA (By similarity). [[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/RS2_THET2 RS2_THET2]] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS18_THET2 RS18_THET2]] Binds as a heterodimer with protein S6 to the central domain of the 16S rRNA, where it helps stabilize the platform of the 30S subunit (By similarity). [[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/RS16_THET2 RS16_THET2]] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [[http://www.uniprot.org/uniprot/RL22_THETH RL22_THETH]] 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).  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 (By similarity). Deleting residues 82 to 84 (the equivalent deletion in E.coli renders cells resistant to erythromycin) would probably cause the tip of the hairpin to penetrate into the tunnel. [[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/RL24_THETH RL24_THETH]] 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.  One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit. [[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/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/RS14Z_THETH RS14Z_THETH]] Binds 16S rRNA, 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). [[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/RS10_THETH RS10_THETH]] Involved in the binding of tRNA to the ribosomes (By similarity). [[http://www.uniprot.org/uniprot/RS11_THET2 RS11_THET2]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RL20_THET2 RL20_THET2]] 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). [[http://www.uniprot.org/uniprot/RL15_THETH RL15_THETH]] Binds to the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RL6_THETH RL6_THETH]] 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 (By similarity).[HAMAP-Rule:MF_01365] [[http://www.uniprot.org/uniprot/RL13_THET2 RL13_THET2]] 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). [[http://www.uniprot.org/uniprot/RS13_THET2 RS13_THET2]] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the 70S ribosome it contacts the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; these bridges are implicated in subunit movement. Contacts the tRNAs in the A and P-sites (By similarity). [[http://www.uniprot.org/uniprot/RL31_THET2 RL31_THET2]] Binds the 23S rRNA (By similarity). [[http://www.uniprot.org/uniprot/RS6_THETH RS6_THETH]] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RL3_THETH RL3_THETH]] 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). [[http://www.uniprot.org/uniprot/RS3_THET2 RS3_THET2]] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [[http://www.uniprot.org/uniprot/RL18_THETH RL18_THETH]] This is one 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 (By similarity). [[http://www.uniprot.org/uniprot/RS9_THET2 RS9_THET2]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RL25_THET2 RL25_THET2]] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance (By similarity). [[http://www.uniprot.org/uniprot/RL5_THETH RL5_THETH]] 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 (By similarity).[HAMAP-Rule:MF_01333_B] [[http://www.uniprot.org/uniprot/RS12_THETH RS12_THETH]] 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 (By similarity).[HAMAP-Rule:MF_00403_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/RS15_THETH RS15_THETH]] 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.  Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [[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/RL2_THET2 RL2_THET2]] 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). [[http://www.uniprot.org/uniprot/RS8_THETH RS8_THETH]] One of the primary rRNA binding proteins, it binds directly to 16S rRNA central domain where it helps coordinate assembly of the platform of the 30S subunit (By similarity). [[http://www.uniprot.org/uniprot/RS4_THET2 RS4_THET2]] 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 (By similarity). [[http://www.uniprot.org/uniprot/RL23_THETH RL23_THETH]] One of the early assembly proteins 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). [[http://www.uniprot.org/uniprot/RL11_THETH RL11_THETH]] This protein binds directly to 23S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RL1_THET8 RL1_THET8]] Directly binds to 23S rRNA. Forms what is known as the L1 stalk, which protrudes beyond the 70S ribosome surface. The stalk is preferentially stabilized in 70S versus 50S crystals. Interacts with the E site tRNA, blocking the exit path. This blockage implies that this section of the ribosome must be able to move to release the deacetylated tRNA.[HAMAP-Rule:MF_01318_B]  Protein L1 is also a translational repressor protein, it controls the translation of the L11 operon by binding to its mRNA (By similarity).[HAMAP-Rule:MF_01318_B] [[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/RS19_THETH RS19_THETH]] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [[http://www.uniprot.org/uniprot/RL21_THET2 RL21_THET2]] This protein binds to 23S rRNA in the presence of protein L20 (By similarity). [[http://www.uniprot.org/uniprot/RS5_THETH RS5_THETH]] 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 (By similarity).[HAMAP-Rule:MF_01307_B] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The universally conserved Gly-Gly-Gln (GGQ) tripeptide in release factors or release factor-like surveillance proteins is required to catalyze the release of nascent peptide in the ribosome. The glutamine of the GGQ is methylated post-translationally at the N(5) position in vivo; this covalent modification is essential for optimal cell growth and efficient translation termination. However, the precise conformation of the methylated-GGQ tripeptide in the ribosome remains unknown. Using cryoEM and X-ray crystallography, we report the conformation of methylated-GGQ in the peptidyl transferase center of the ribosome during canonical translational termination and co-translation quality control. It has been suggested that the GGQ motif arose independently through convergent evolution among otherwise unrelated proteins that catalyze peptide release. The requirement for this tripeptide in the highly conserved peptidyl transferase center suggests that the conformation reported here is likely shared during termination of protein synthesis in all domains of life.

Conformation of methylated GGQ in the Peptidyl Transferase Center during Translation Termination.,Zeng F, Jin H Sci Rep. 2018 Feb 5;8(1):2349. doi: 10.1038/s41598-018-20107-8. PMID:29403017<ref>PMID:29403017</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 6c5l" style="background-color:#fffaf0;"></div>

==See Also==
*[[Ribosome 3D structures|Ribosome 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Flavobacterium thermophilum yoshida and oshima 1971]]
[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Jin, H]]
[[Category: Zeng, F]]
[[Category: Methylated rf2]]
[[Category: Ribosome]]
[[Category: Translation termination]]