PDBsum entry 2aar

Ribosome

PDB id: 2aar

Contents

Protein chains

93 a.a.* *

65 a.a.* *

113 a.a.* *

DNA/RNA

* Residue conservation analysis

* C-alpha coords only

PDB id:

2aar

Name:

Ribosome

Title:

Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome.

Structure:

23s ribosomal RNA. Chain: 0. 50s ribosomal protein l23. Chain: r. 50s ribosomal protein l29. Chain: w. Trigger factor. Chain: 7. Fragment: n-terminal domain.

Source:

Deinococcus radiodurans. Organism_taxid: 1299. Organism_taxid: 1299

Biol. unit:

Tetramer (from PQS)

Resolution:

3.50Å R-factor: 0.251 R-free: 0.320

Authors:

D.Baram,E.Pyetan,A.Sittner,T.Auerbach-Nevo,A.Bashan,A.Yonath

Key ref:

D.Baram et al. (2005). Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action. Proc Natl Acad Sci U S A, 102, 12017-12022. PubMed id: 16091460 DOI: 10.1073/pnas.0505581102

Date:

14-Jul-05 Release date: 23-Aug-05

Protein chain

Q9RXK0  (RL23_DEIRA) -  Large ribosomal subunit protein uL23 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 95 a.a.

Struc: 93 a.a.

Protein chain

Q9RXJ4  (RL29_DEIRA) -  Large ribosomal subunit protein uL29 from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 67 a.a.

Struc: 65 a.a.

Protein chain

Q9RT21  (TIG_DEIRA) -  Trigger factor from Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)

Seq: 465 a.a.

Struc: 113 a.a.

DNA/RNA chain

G-G-U-C-A-A-G-A-U-A-G-U-A-A-G-G-G-U-C-C-A-C-G-G-U-G-G-A-U-G-C-C-C-U-G-G-C-G-C- ... 2766 bases

Enzyme reactions

• Enzyme class 1: Chain 7: E.C.5.2.1.8 - peptidylprolyl isomerase.
• Reaction: [protein]-peptidylproline (omega=180) = [protein]-peptidylproline (omega=0)
• Enzyme class 2: Chains R, W: E.C.?

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1073/pnas.0505581102

Proc Natl Acad Sci U S A 102:12017-12022 (2005)

PubMed id: 16091460

Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action.

D.Baram, E.Pyetan, A.Sittner, T.Auerbach-Nevo, A.Bashan, A.Yonath.

ABSTRACT

Trigger factor (TF), the first chaperone in eubacteria to encounter the emerging nascent chain, binds to the large ribosomal subunit in the vicinity of the protein exit tunnel opening and forms a sheltered folding space. Here, we present the 3.5-A crystal structure of the physiological complex of the large ribosomal subunit from the eubacterium Deinococcus radiodurans with the N-terminal domain of TF (TFa) from the same organism. For anchoring, TFa exploits a small ribosomal surface area in the vicinity of proteins L23 and L29, by using its "signature motif" as well as additional structural elements. The molecular details of TFa interactions reveal that L23 is essential for the association of TF with the ribosome and may serve as a channel of communication with the nascent chain progressing in the tunnel. L29 appears to induce a conformational change in TFa, which results in the exposure of TFa hydrophobic patches to the opening of the ribosomal exit tunnel, thus increasing its affinity for hydrophobic segments of the emerging nascent polypeptide. This observation implies that, in addition to creating a protected folding space for the emerging nascent chain, TF association with the ribosome prevents aggregation by providing a competing hydrophobic environment and may be critical for attaining the functional conformation necessary for chaperone activity.

Selected figure(s)

Figure 2.
Fig. 2. The crystallographic structure of bound TFa. (a) Structure of TFa upon association with the ribosome. (b) An unbiased 2F[o] - F[c] electron density map around helix A1, contoured at 1.5 .

Figure 4.
Fig. 4. Detailed molecular interactions of TFa (orange) with ribosomal proteins L23 (blue) (a and b) and L29 (magenta) (c).

Figures were selected by an automated process.