InterPro domain: IPR016031

The tryptophan RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in Bacillus sp. by binding to the leader region of the nascent trp operon mRNA [ 1 ]. The crystal structure of the Trp RNA-binding attenuation protein of Bacillus subtilis (mtrB, P19466 ) has been solved [ 2 ]. TRAP forms an oligomeric ring consisting of 11 single-domain subunits, where each subunit adopts a double-stranded beta-helix structure with the appearance of a beta-sandwich of distinct architecture and jelly-roll fold. The 11 subunits are stabilised by 11 inter-subunit strands, forming a beta-wheel with a large central hole. TRAP is activated by binding to tryptophan in clefts between adjacent beta-strands, which induces conformational changes in the protein. Activated TRAP binds an mRNA target sequence consisting of 11 (G/U)AG repeats, separated by 2-3 spacer nucleotides. The spacer nucleotides do not make direct contact with the TRAP protein, but they do influence the conformation of the RNA, which might influence the specificity of TRAP [ 3 ].

This superfamily represents a domain with a TRAP-like double-stranded beta-helix topology. This domain is found in TRAP proteins, as well as in the hypothetical protein SPyM3_0169 from Streptococcus pyogenes. SPyM3_0169 contains 9 domains per ring-like trimer, where each subunit contains three structural repeats.

1. Specificity of TRAP-RNA interactions: crystal structures of two complexes with different RNA sequences. Acta Crystallogr. D Biol. Crystallogr. 58, 615-21
2. The structure of trp RNA-binding attenuation protein. Nature 374, 693-700
3. The interaction of RNA with TRAP: the role of triplet repeats and separating spacer nucleotides. J. Mol. Biol. 338, 43-53