PDBsum entry 2fow

Ribosome

PDB id: 2fow

Contents

Protein chain

76 a.a.

References listed in PDB file

Key reference

Title

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.

Authors

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

Ref.

J Mol Biol, 1997, 274, 101-113. [DOI no: 10.1006/jmbi.1997.1379]

PubMed id

9398519

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a percentage match of 97%.

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.

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.