5uz4 | pdb_00005uz4
The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly
Structural highlights
Function[RS12_ECO45] With S4 and S5 plays an important role in translational accuracy.[HAMAP-Rule:MF_00403] 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] [RSGA_ECOLI] One of at least 4 proteins (Era, RbfA, RimM and RsgA/YjeQ) that assist in the late maturation steps of the functional core of the 30S ribosomal subunit (PubMed:18223068, PubMed:21102555, PubMed:21303937, PubMed:25904134, PubMed:27382067). Binds the 30S subunit contacting the head, platform, and rRNA helix 44, which may assist the last maturation stages (PubMed:21788480, PubMed:21960487). Removes RbfA from mature, but not immature 30S ribosomes in a GTP-dependent manner; 95% removal in the presence of GTP, 90% removal in GMP-PNP and 65% removal in the presence of GDP (PubMed:21102555, PubMed:25904134). Circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover (PubMed:12220175). Dispensible for viability, but important for overall fitness. The intrinsic GTPase activity is stimulated by the presence of 30S (160-fold increase in kcat) or 70S (96-fold increase in kcat) ribosomes (PubMed:14973029). Mature 30S ribosomes stimulate intrinsic GTPase more than do immature 30S ribosomes (PubMed:25904134). Ribosome-associated GTPase activity is stimulated by RbfA (PubMed:21102555). The GTPase is inhibited by aminoglycoside antibiotics such as neomycin and paromycin (PubMed:15466596) streptomycin and spectinomycin (PubMed:15828870). This inhibition is not due to competition for binding sites on the 30S or 70S ribosome (PubMed:15828870).[1] [2] [3] [4] [5] [6] [7] [8] [RS8_ECO45] 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. [RS3_ECO45] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation. [RS18_ECO45] 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. [RS19_ECO45] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA. [RS14_ECO45] 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. [RS17_ECO45] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA. [RS7_ECOLI] 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, where it has been shown to contact mRNA. Has been shown to contact tRNA in both the P and E sites; it probably blocks exit of the E site tRNA.[9] Protein S7 is also a translational repressor protein; it regulates the expression of the str operon members to different degrees by binding to its mRNA.[10] [RS4_ECO45] One of the primary rRNA binding proteins, it binds directly to 16S rRNA where it nucleates assembly of the body of the 30S subunit. With S5 and S12 plays an important role in translational accuracy. [RS10_ECO45] Involved in the binding of tRNA to the ribosomes. [RS13_ECO57] Located at the top of the head of the 30S subunit, it contacts several helices of the 16S rRNA. In the E.coli 70S ribosome in the initiation state it has been modeled to contact the 23S rRNA (bridge B1a) and protein L5 of the 50S subunit (bridge B1b), connecting the 2 subunits; bridge B1a is broken in the model with bound EF-G, while the protein-protein contacts between S13 and L5 in B1b change. Contacts the tRNAs in the A and P sites (By similarity). [RS15_ECO57] 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). Forms an intersubunit bridge (bridge B4) with the 23S rRNA of the 50S subunit in the ribosome (By similarity). [RS5_ECO57] With S4 and S12 plays an important role in translational accuracy. Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body. [RS11_ECO45] Located on the platform of the 30S subunit, it bridges several disparate RNA helices of the 16S rRNA. Forms part of the Shine-Dalgarno cleft in the 70S ribosome. [RS20_ECO45] Binds directly to 16S ribosomal RNA. [RS6_ECOLI] Binds together with S18 to 16S ribosomal RNA.[HAMAP-Rule:MF_00360] Publication Abstract from PubMedRecent work suggests that bacterial YjeQ (RsgA) participates in the late stages of assembly of the 30S subunit and aids the assembly of the decoding center but also binds the mature 30S subunit with high affinity. To determine the function and mechanisms of YjeQ in the context of the mature subunit, we determined the cryo-EM structure of the fully assembled 30S subunit in complex with YjeQ at 5.8-A resolution. We found that binding of YjeQ stabilizes helix 44 into a conformation similar to that adopted by the subunit during proofreading. This finding indicates that, along with acting as an assembly factor, YjeQ has a role as a checkpoint protein, consisting of testing the proofreading ability of the 30S subunit. The structure also informs the mechanism by which YjeQ implements the release from the 30S subunit of a second assembly factor, called RbfA. Finally, it reveals how the 30S subunit stimulates YjeQ GTPase activity and leads to release of the protein. Checkpoint functions have been described for eukaryotic ribosome assembly factors; however, this work describes an example of a bacterial assembly factor that tests a specific translation mechanism of the 30S subunit. The cryo-EM structure of YjeQ bound to the 30S subunit suggests a fidelity checkpoint function for this protein in ribosome assembly.,Razi A, Guarne A, Ortega J Proc Natl Acad Sci U S A. 2017 Apr 25;114(17):E3396-E3403. doi:, 10.1073/pnas.1618016114. Epub 2017 Apr 10. PMID:28396444[11] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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