6dzp | pdb_00006dzp
Cryo-EM Structure of Mycobacterium smegmatis C(minus) 50S ribosomal subunit
Structural highlights
Function[RL23_MYCS2] 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.[HAMAP-Rule:MF_01369] [RL6_MYCS2] 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. [RL19_MYCS2] This protein is located at the 30S-50S ribosomal subunit interface and may play a role in the structure and function of the aminoacyl-tRNA binding site. [RL20_MYCS2] 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. [I7FGD9_MYCS2] 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.[HAMAP-Rule:MF_01337] [RL22_MYCS2] 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] The globular domain of the protein is located near the polypeptide exit tunnel on the outside of the subunit, while an extended beta-hairpin is found that lines the wall of the exit tunnel in the center of the 70S ribosome.[HAMAP-Rule:MF_01331] [RL16_MYCS2] Binds 23S rRNA and is also seen to make contacts with the A and possibly P site tRNAs. [RL11_MYCS2] Forms part of the ribosomal stalk which helps the ribosome interact with GTP-bound translation factors.[HAMAP-Rule:MF_00736] [RL13_MYCS2] 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.[HAMAP-Rule:MF_01366] [RL24_MYCS2] 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. [A0QSG8_MYCS2] Binds to the 23S rRNA.[HAMAP-Rule:MF_01341][SAAS:SAAS00687840] [A0R3D2_MYCS2] This is one of the proteins that binds to the 5S RNA in the ribosome where it forms part of the central protuberance.[HAMAP-Rule:MF_01334][SAAS:SAAS00720025] [RL5_MYCS2] 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 (bridge B1b), connecting the 2 subunits; this bridge is implicated in subunit movement. Contacts the P site tRNA; the 5S rRNA and some of its associated proteins might help stabilize positioning of ribosome-bound tRNAs.[HAMAP-Rule:MF_01333] [RL2_MYCS2] 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. [RL10_MYCS2] Forms part of the ribosomal stalk, playing a central role in the interaction of the ribosome with GTP-bound translation factors. [RL14_MYCS2] Binds to 23S rRNA. Forms part of two intersubunit bridges in the 70S ribosome. [RL9_MYCS2] Binds to the 23S rRNA. [RL3_MYCS2] 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. [RL21_MYCS2] This protein binds to 23S rRNA in the presence of protein L20.[HAMAP-Rule:MF_01363] [RL4_MYCS2] 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.[HAMAP-Rule:MF_01328] Forms part of the polypeptide exit tunnel.[HAMAP-Rule:MF_01328] Publication Abstract from PubMedBacteria respond to zinc starvation by replacing ribosomal proteins that have the zinc-binding CXXC motif (C+) with their zinc-free (C-) paralogues. Consequences of this process beyond zinc homeostasis are unknown. Here, we show that the C- ribosome in Mycobacterium smegmatis is the exclusive target of a bacterial protein Y homolog, referred to as mycobacterial-specific protein Y (MPY), which binds to the decoding region of the 30S subunit, thereby inactivating the ribosome. MPY binding is dependent on another mycobacterial protein, MPY recruitment factor (MRF), which is induced on zinc depletion, and interacts with C- ribosomes. MPY binding confers structural stability to C- ribosomes, promoting survival of growth-arrested cells under zinc-limiting conditions. Binding of MPY also has direct influence on the dynamics of aminoglycoside-binding pockets of the C- ribosome to inhibit binding of these antibiotics. Together, our data suggest that zinc limitation leads to ribosome hibernation and aminoglycoside resistance in mycobacteria. Furthermore, our observation of the expression of the proteins of C- ribosomes in Mycobacterium tuberculosis in a mouse model of infection suggests that ribosome hibernation could be relevant in our understanding of persistence and drug tolerance of the pathogen encountered during chemotherapy of TB. Zinc depletion induces ribosome hibernation in mycobacteria.,Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):8191-8196. doi:, 10.1073/pnas.1804555115. Epub 2018 Jul 23. PMID:30038002[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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