PDBsum entry 1k8h

RNA binding protein

PDB id: 1k8h

Contents

Protein chain

133 a.a. *

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structure of small protein b: the protein component of the tmrna-Smpb system for ribosome rescue.

Authors

G.Dong, J.Nowakowski, D.W.Hoffman.

Ref.

EMBO J, 2002, 21, 1845-1854. [DOI no: 10.1093/emboj/21.7.1845]

PubMed id

11927568

Abstract

Small protein B (SmpB) is an essential component of the highly conserved tmRNA-SmpB system that has the dual function of releasing stalled ribosomes from damaged messenger RNAs and targeting incompletely synthesized protein fragments for degradation. Nuclear magnetic resonance (NMR) analysis of SmpB from Aquifex aeolicus revealed an antiparallel beta-barrel structure, with three helices packed outside the core of the barrel. While the overall structure of SmpB appears to be unique, the structure does contain an embedded oligonucleotide binding fold; in this respect SmpB has similarity to several other RNA-binding proteins that are known to be associated with translation, including IF1, ribosomal protein S17 and the N-terminal domain of aspartyl tRNA synthetase. Conserved amino acids on the protein surface that are most likely to directly interact with the tmRNA were identified. The presence of widely separated clusters of conserved amino acids suggests that SmpB could function either by stabilizing two distal regions of the tmRNA, or by facilitating an interaction between the tmRNA and another component of the translational apparatus.

Figure 5.
Figure 5 -sheet structure of the SmpB protein. Note that strand 5 appears twice in the figure, to show its anti-parallel arrangement relative to strands 2 and 4, completing the closed -barrel structure. Some of the pairs of protons for which NOE cross peaks are observed are indicated by lines. Inter-strand hydrogen bonds are indicated by dotted lines.

Figure 6.
Figure 6 Stereoview ribbon diagrams of SmpB. The two views differ by a 90° rotation. The protein is color-ramped from blue at the N-terminus to red at the C-terminus. The coordinates for SmpB have been submitted to the Protein Data Bank and have been assigned PDB code 1K8H. The diagram was created using MOLSCRIPT (Kraulis, 1991).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 1845-1854) copyright 2002.