4kfk

From Proteopedia

Jump to: navigation, search
Warning: this is a large structure, and loading might take a long time or not happen at all.
4kfk, resolution 3.40Å ()
Ligands: ,
Gene: TT_C1852 (THET2)
Related: 4kfh, 4kfi, 4kfl


Resources: FirstGlance, OCA, RCSB, PDBsum
Coordinates: save as pdb, mmCIF, xml


Contents

Crystal structure of the 70S ribosome bound with the Q253P mutant of release factor RF2. 30S of the B subunit

Publication Abstract from PubMed

Bacterial translation termination is mediated by release factors RF1 and RF2, which recognize stop codons and catalyze hydrolysis of the peptidyl-tRNA ester bond. The catalytic mechanism has been debated. We proposed that the backbone amide NH group, rather than the side chain, of the glutamine of the universally conserved GGQ motif participates in catalysis by H-bonding to the tetrahedral transition-state intermediate and by product stabilization. This was supported by complete loss of RF1 catalytic activity when glutamine is replaced by proline, the only residue that lacks a backbone NH group. Here, we present the 3.4 A crystal structure of the ribosome complex containing the RF2 Q253P mutant and find that its fold, including the GGP sequence, is virtually identical to that of wild-type RF2. This rules out proline-induced misfolding and further supports the proposal that catalytic activity requires interaction of the Gln-253 backbone amide with the 3' end of peptidyl-tRNA.

Crystal Structure of the 70S Ribosome Bound with the Q253P Mutant Form of Release Factor RF2., Santos N, Zhu J, Donohue JP, Korostelev AA, Noller HF, Structure. 2013 Jun 12. pii: S0969-2126(13)00158-5. doi:, 10.1016/j.str.2013.04.028. PMID:23769667

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

Function

[RS8_THET2] 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). [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). [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). [RS14Z_THET2] 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). [RS19_THET2] Protein S19 forms a complex with S13 that binds strongly to the 16S ribosomal RNA (By similarity). [RS15_THET2] 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). [RS20_THET2] Binds directly to 16S ribosomal RNA (By similarity). [RS10_THET2] Involved in the binding of tRNA to the ribosomes (By similarity). [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). [RS3_THET2] Binds the lower part of the 30S subunit head. Binds mRNA in the 70S ribosome, positioning it for translation (By similarity). [RS6_THET2] Located on the outer edge of the platform on the body of the 30S subunit (By similarity). [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). [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). [RS12_THET2] With S4 and S5 plays an important role in translational accuracy (By similarity). 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). [RS17_THET2] One of the primary rRNA binding proteins, it binds specifically to the 5'-end of 16S ribosomal RNA (By similarity). [RS5_THET2] With S4 and S12 plays an important role in translational accuracy (By similarity). Located at the back of the 30S subunit body where it stabilizes the conformation of the head with respect to the body (By similarity). [Q72GJ6_THET2] Peptide chain release factor 2 directs the termination of translation in response to the peptide chain termination codons UGA and UAA (By similarity). [RSHX_THET2] 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). [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). [RS16_THET2] Binds to the lower part of the body of the 30S subunit, where it stabilizes two of its domains (By similarity). [RS2_THET2] Spans the head-body hinge region of the 30S subunit. Is loosely associated with the 30S subunit (By similarity).

About this Structure

4kfk is a 24 chain structure with sequence from Thet2 and Thermus thermophilus. Full crystallographic information is available from OCA.

See Also

Reference

  • Santos N, Zhu J, Donohue JP, Korostelev AA, Noller HF. Crystal Structure of the 70S Ribosome Bound with the Q253P Mutant Form of Release Factor RF2. Structure. 2013 Jun 12. pii: S0969-2126(13)00158-5. doi:, 10.1016/j.str.2013.04.028. PMID:23769667 doi:10.1016/j.str.2013.04.028

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools