1K8H

NMR Structure of Small Protein B (SmpB) from Aquifex aeolicus

Summary for 1K8H

• Entry DOI: 10.2210/pdb1k8h/pdb
• Descriptor: Small protein B (1 entity in total)
• Functional Keywords: smpb, ssra associated protein, rna binding protein
• Biological source: Aquifex aeolicus
• Cellular location: Cytoplasm (Potential): O66640
• Total number of polymer chains: 1
• Total formula weight: 15523.29

Authors

Dong, G.,Hoffman, D.W. (deposition date: 2001-10-24, release date: 2002-03-20, Last modification date: 2024-05-22)

Primary citation

Dong, G.,Nowakowski, J.,Hoffman, D.W.
Structure of small protein B: the protein component of the tmRNA-SmpB system for ribosome rescue.
EMBO J., 21:1845-1854, 2002

PubMed 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.

PubMed: 11927568
DOI: 10.1093/emboj/21.7.1845

Experimental method

SOLUTION NMR