PDBsum entry 2fow

Ribosome

PDB id: 2fow

Contents

Protein chain

76 a.a. *

* Residue conservation analysis

PDB id:

2fow

Name:

Ribosome

Title:

The RNA binding domain of ribosomal protein l11: three-dimensional structure of the RNA-bound form of the protein, nmr, 26 structures

Structure:

Ribosomal protein l11. Chain: a. Fragment: c-terminal domain, 75 residues. Engineered: yes. Mutation: yes. Other_details: structure of the protein in this entry was determined as a 1\:1 complex with its target RNA of 58 nucleotides, bases 1051 - 1108 of the e. Coli sequence

Source:

Geobacillus stearothermophilus. Organism_taxid: 1422. Cell_line: bl21. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

26 models

Authors:

A.P.Hinck,M.A.Markus,S.Huang,S.Grzesiek,I.Kustanovich,D.E.Draper, D.A.Torchia

Key ref:

A.P.Hinck et al. (1997). The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA. J Mol Biol, 274, 101-113. PubMed id: 9398519 DOI: 10.1006/jmbi.1997.1379

Date:

26-May-97 Release date: 26-Nov-97

Protein chain

P56210  (RL11_GEOSE) -  Large ribosomal subunit protein uL11 (Fragment) from Geobacillus stearothermophilus

Seq: 133 a.a.

Struc: 76 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1006/jmbi.1997.1379

J Mol Biol 274:101-113 (1997)

PubMed id: 9398519

The RNA binding domain of ribosomal protein L11: three-dimensional structure of the RNA-bound form of the protein and its interaction with 23 S rRNA.

A.P.Hinck, M.A.Markus, S.Huang, S.Grzesiek, I.Kustonovich, D.E.Draper, D.A.Torchia.

ABSTRACT

The three-dimensional solution structure has been determined by NMR spectroscopy of the 75 residue C-terminal domain of ribosomal protein L11 (L11-C76) in its RNA-bound state. L11-C76 recognizes and binds tightly to a highly conserved 58 nucleotide domain of 23 S ribosomal RNA, whose secondary structure consists of three helical stems and a central junction loop. The NMR data reveal that the conserved structural core of the protein, which consists of a bundle of three alpha-helices and a two-stranded parallel beta-sheet four residues in length, is nearly the same as the solution structure determined for the non-liganded form of the protein. There are however, substantial chemical shift perturbations which accompany RNA binding, the largest of which map onto an extended loop which bridges the C-terminal end of alpha-helix 1 and the first strand of parallel beta-sheet. Substantial shift perturbations are also observed in the N-terminal end of alpha-helix 1, the intervening loop that bridges helices 2 and 3, and alpha-helix 3. The four contact regions identified by the shift perturbation data also displayed protein-RNA NOEs, as identified by isotope-filtered three-dimensional NOE spectroscopy. The shift perturbation and NOE data not only implicate helix 3 as playing an important role in RNA binding, but also indicate that regions flanking helix 3 are involved as well. Loop 1 is of particular interest as it was found to be flexible and disordered for L11-C76 free in solution, but not in the RNA-bound form of the protein, where it appears rigid and adopts a specific conformation as a result of its direct contact to RNA.

Selected figure(s)

Figure 1.
Figure 1. Ribosomal RNA and L11 sequences used for NMR studies and a comparison of L11-RNA and homeodo- main-DNA contact sites. (a) A 58 nucleotide fragment of E. coli 23 S rRNA, modified at position 1061 (E. coli number- ing) by a U to A substitution. Bases which are protected by native L11 in hydroxyl radical footprinting experiments are indicated by gray shading (Rosendahl & Douthwaite, 1993). (b) A primary sequence alignment of the Oct-1 (Klemm et al., 1994) and MAT-a2 (Li et al., 1995) homeodomains. Homeodomain residues are numbered according the convention previously established (Li et al., 1995). The helical boundaries and amino acid residues which contact the DNA, are those reported for the Oct-1 (Klemm et al., 1994) and MAT-a2 (Li et al., 1995) homeodomain-DNA com- plexes, respectively. The three helical regions are indicated symbolically above the amino acid sequences, whereas the protein-DNA contact sites are identified by residue shading. Residues shaded black correspond to those which engage in base-specific contacts, whereas those shaded gray correspond to those which exhibit either phosphate or ribose contacts. (c) Primary sequence, deduced secondary structure,and sites of protein-RNA contacts for the C-term- inal fragment (75 residues plus N-terminal initiator methionine) of Bacillus stearothermophilus L11. The secondary structure is indicated schematically above the amino acid sequence, whereas the protein-RNA contact sites are indi- cated by residue shading. The latter were identified on the basis of filtered NOE experiments, as described in Materials and Methods.

Figure 6.
Figure 6. A comparison of the backbone C a traces for fL11-C76 (Markus et al., 1997) to bL11-C76. The struc- tures have been superimposed on the basis of the deduced secondary structure of bL11-C76 (residues 10 to 17, 33 to 46, 56 to 67, and 72 to 75). bL11-C76 is indi- cated by a continuous line, whereas, fL11-C76 is indi- cated by a broken line. Residues are numbered according to the starting and ending points of the regu- lar secondary structure of bL11-C76.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1997, 274, 101-113) copyright 1997.

Figures were selected by an automated process.