4v8a | pdb_00004v8a
The structure of thermorubin in complex with the 70S ribosome from Thermus thermophilus.
Structural highlights
Function[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] [RS2_THET8] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit.[HAMAP-Rule:MF_00291_B] [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] [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] [RL31_THET8] Binds the 23S rRNA (By similarity).[HAMAP-Rule:MF_00501] [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] [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] [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] [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] [RL32_THET8] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00340] [RL33_THET8] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00294] Contacts the E site tRNA.[HAMAP-Rule:MF_00294] [RS10_THET8] Part of the top of the 30S subunit head.[HAMAP-Rule:MF_00508] [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] [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] [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] [RL29_THET8] One of the proteins that surrounds the polypeptide exit tunnel on the outside of the subunit.[HAMAP-Rule:MF_00374] [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] [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] [RL15_THET8] Binds to the 23S rRNA (By similarity).[HAMAP-Rule:MF_01341_B] [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] [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] [RL27_THET8] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00539] [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] [RL34_THET8] Found on the solvent side of the large subunit.[HAMAP-Rule:MF_00391] [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] [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] [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] [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] [RS6_THET8] Located on the outer edge of the platform on the body of the 30S subunit.[HAMAP-Rule:MF_00360] [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] [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. [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] [RL16_THET8] This protein binds directly to 23S rRNA. Interacts with the A site tRNA.[HAMAP-Rule:MF_01342] [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] [RL19_THET8] Contacts the 16S rRNA of the 30S subunit (part of bridge B6), connecting the 2 subunits.[HAMAP-Rule:MF_00402] [RL9_THET8] Binds to the 23S rRNA. Extends more that 50 Angstroms beyond the surface of the 70S ribosome.[HAMAP-Rule:MF_00503] [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] [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] [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] [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] [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] [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] [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] [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] Publication Abstract from PubMedThermorubin is a small-molecule inhibitor of bacterial protein synthesis, but relatively little is known about the molecular mechanism by which it blocks translation. The structure of the complex between thermorubin and the 70S ribosome from Thermus thermophilus reported here shows that thermorubin interacts with the ribosome in a way that is distinct from any other known class of ribosome inhibitor. Though it is structurally similar to tetracycline, it binds to the ribosome at an entirely different location-the interface between the small and large subunits that is formed by inter-subunit bridge B2a. This region of the ribosome is known to play a role in the initiation of translation, and thus, the binding site we observe is consistent with evidence suggesting that thermorubin inhibits the initiation stage of protein synthesis. The binding of thermorubin induces a rearrangement of two bases on helix 69 of the 23S rRNA, and presumably, this rearrangement blocks the binding of an A-site tRNA, thereby inhibiting peptide bond formation. Due in part to its low solubility in aqueous media, thermorubin has not been used clinically, although it is a potent antibacterial agent with low toxicity (Therapeutic Index>200). The interactions between thermorubin and the ribosome, as well as its adjacency to the observed binding sites of three other antibiotic classes, may enable the design of novel derivatives that share thermorubin's mode of action but possess improved pharmacodynamic properties. The Antibiotic Thermorubin Inhibits Protein Synthesis by Binding to Inter-Subunit Bridge B2a of the Ribosome.,Bulkley D, Johnson F, Steitz TA J Mol Biol. 2012 Jan 2. PMID:22240456[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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