PDBsum entry 2e34

RNA binding protein

PDB id: 2e34

Contents

Protein chain

147 a.a. *

* Residue conservation analysis

PDB id:

2e34

Name:

RNA binding protein

Title:

L11 structure with rdc and rg refinement

Structure:

50s ribosomal protein l11. Chain: a. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli. Expression_system_taxid: 562

NMR struc:

20 models

Authors:

D.Lee,J.D.Walsh,P.Yu,M.A.Markus,T.Choli-Papadopoulous,C.D.Schwieters, S.Krueger,D.E.Draper,Y.X.Wang

Key ref:

D.Lee et al. (2007). The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes. J Mol Biol, 367, 1007-1022. PubMed id: 17292917 DOI: 10.1016/j.jmb.2007.01.013

Date:

20-Nov-06 Release date: 19-Jun-07

Protein chain

P36238  (RL11_THETH) -  Large ribosomal subunit protein uL11 from Thermus thermophilus

Seq: 147 a.a.

Struc: 147 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.jmb.2007.01.013

J Mol Biol 367:1007-1022 (2007)

PubMed id: 17292917

The structure of free L11 and functional dynamics of L11 in free, L11-rRNA(58 nt) binary and L11-rRNA(58 nt)-thiostrepton ternary complexes.

D.Lee, J.D.Walsh, P.Yu, M.A.Markus, T.Choli-Papadopoulou, C.D.Schwieters, S.Krueger, D.E.Draper, Y.X.Wang.

ABSTRACT

The L11 binding site is one of the most important functional sites in the ribosome. The N-terminal domain of L11 has been implicated as a "reversible switch" in facilitating the coordinated movements associated with EF-G-driven GTP hydrolysis. The reversible switch mechanism has been hypothesized to require conformational flexibility involving re-orientation and re-positioning of the two L11 domains, and warrants a close examination of the structure and dynamics of L11. Here we report the solution structure of free L11, and relaxation studies of free L11, L11 complexed to its 58 nt RNA recognition site, and L11 in a ternary complex with the RNA and thiostrepton antibiotic. The binding site of thiostrepton on L11 was also defined by analysis of structural and dynamics data and chemical shift mapping. The conclusions of this work are as follows: first, the binding of L11 to RNA leads to sizable conformation changes in the regions flanking the linker and in the hinge area that links a beta-sheet and a 3(10)-helix-turn-helix element in the N terminus. Concurrently, the change in the relative orientation may lead to re-positioning of the N terminus, as implied by a decrease of radius of gyration from 18.5 A to 16.2 A. Second, the regions, which undergo large conformation changes, exhibit motions on milliseconds-microseconds or nanoseconds-picoseconds time scales. Third, binding of thiostrepton results in more rigid conformations near the linker (Thr71) and near its putative binding site (Leu12). Lastly, conformational changes in the putative thiostrepton binding site are implicated by the re-emergence of cross-correlation peaks in the spectrum of the ternary complex, which were missing in that of the binary complex. Our combined analysis of both the chemical shift perturbation and dynamics data clearly indicates that thiostrepton binds to a pocket involving residues in the 3(10)-helix in L11.

Selected figure(s)

Figure 4.
Figure 4. Comparison of torsion angles between the solution structure and the crystal and the View the MathML source- [0?wchp=dGLzVtb-zSkzV] structure of L11. Residue regions showing Δ[ang] > vert, similar 50° are indicated. Figure 4. Comparison of torsion angles between the solution structure and the crystal and the [3]Image structure of L11. Residue regions showing Δ[ang] > [4]not, vert, similar 50° are indicated.

Figure 9.
Figure 9. The molecular surface and ribbon diagram of L11. Residues whose chemical shifts of backbone amide groups either re-emerged or were significantly perturbed upon thiostrepton binding are indicated by their residue numbers and magenta color in the ribbon diagram. The Pro21 and Pro22 positions in the structure are also indicated. The position of Tyr60 is indicated at the back of the N terminus. Figure 9. The molecular surface and ribbon diagram of L11. Residues whose chemical shifts of backbone amide groups either re-emerged or were significantly perturbed upon thiostrepton binding are indicated by their residue numbers and magenta color in the ribbon diagram. The Pro21 and Pro22 positions in the structure are also indicated. The position of Tyr60 is indicated at the back of the N terminus.

The above figures are reprinted from an Open Access publication published by Elsevier: J Mol Biol (2007, 367, 1007-1022) copyright 2007.

Figures were selected by an automated process.