Protein Name

Trp RNA-Binding Attenuation Protein/RNA complex


Bacillus stearothermophilus (bacteria)

Biological Context

Bacteria have a cooperative transcription-translation regulation system called "attenuation" as their control system for gene expression. The tryptophan operon of E.coli is regulated simultaneously both by the trp repressor system and by attenuation. In the case of E.coli attenuation, regulation is achieved by exchange of the stem-loop structures of the attenuation region, which is located between the structural gene trpE and the promoter gene on the transcript mRNA, depending on the tryptophan concentration in cells. When cellular tryptophan concentrations are too high, stem-loop structures for transcription termination are formed and transcription by RNA polymerase is terminated at the attenuation regions. On the other hand, when tryptophan is deficient in cells, ribosomes are stuck for a while on the tryptophan-codon rich region just prior to transcriptional elongation since in bacteria translation immediately follow transcription. Thus anti-transcription termination structures are formed instead of transcription termination stem-loops and the trpE gene will be transcribed. Bacillus subtilis does not have an E.coli-like trp repressor dependent regulation system. The trp gene expression is regulated by attenuation only, and the mechanism is different as well. In B. subtilis, under the condition of tryptophan excess, trp RNA-binding attenuation protein (TRAP), which do not exist in E.coli and other enterobacteria, bind to the attenuation region to form the transcription termination structure. TRAP binds a specific RNA sequence, only when activated by L-tryptophan binding. Since the ribosome-binding site is included in an RNA hairpin, expression is also regulated at the ribosomal translation level. TRAP also regulates translation of trpG, which is located in an operon involved in folic acid biosynthesis. In this case the Shine-Dalgarno sequence is located within the TRAP binding site, hence more directly inhibits ribosome binding to RNA.

Structure Description


This structure is the complex between TRAP from Bacillus stearothermophilus and a 53-base single-stranded RNA. TRAP forms a complex of eleven identical subunits, arranged in a symmetrical ring with a diameter of about 80 angstroms. Each subunit has one bound L-tryptophan. Each of these L-tryptophans is bound between adjacent subunits with every possible hydrogen bond made and with the indole moiety buried inside an intersubunit hydrophobic pocket. The target RNA contains eleven triplets separated by two or three bases long variable 'spacer' sequences. Each of these triprets, which are almost exclusively made up of GAG or UAG, binds to one of the subunits of TRAP. The RNA itself does not adopt any secondary structure but is wrapped around TRAP. TRAP interacts with RNA thourgh the bases and there are no direct interactions with phosphates.

Protein Data Bank (PDB)



Antson, A.A. Dodson, E.J. Dodson, G. Greaves, R.B. Chen, X. Gollnick, P.; "Structure of the trp RNA-binding attenuation protein, TRAP, bound to RNA."; Nature; (1999) 401:235-242 PubMed:10499579.


author: Tomoki Matsuda

Japanese version:PDB:1C9S