Regulatory Features of the TRP Operon and the Crystal Structure of the TRP RNA-Binding Attenuation Protein from Bacillus Stearothermophilus.

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.215 

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Regulatory features of the trp operon and the crystal structure of the trp RNA-binding attenuation protein from Bacillus stearothermophilus.

Chen, X.Antson, A.A.Yang, M.Li, P.Baumann, C.Dodson, E.J.Dodson, G.G.Gollnick, P.

(1999) J Mol Biol 289: 1003-1016

  • DOI: https://doi.org/10.1006/jmbi.1999.2834
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Characterization of both the cis and trans -acting regulatory elements indicates that the Bacillus stearothermophilustrp operon is regulated by an attenuation mechanism similar to that which controls the trp operon in Bacillus subtilis. Secondary structure predictions indicate that the leader region of the trp mRNA is capable of folding into terminator and anti- terminator RNA structures. B. stearothermophilus also encodes an RNA-binding protein with 77% sequence identity with the RNA-binding protein (TRAP) that regulates attenuation in B. subtilis. The X-ray structure of this protein has been determined in complex with L-tryptophan at 2.5 A resolution. Like the B. subtilis protein, B. stearothermophilus TRAP has 11 subunits arranged in a ring-like structure. The central cavities in these two structures have different sizes and opposite charge distributions, and packing within the B. stearothermophilus TRAP crystal form does not generate the head-to-head dimers seen in the B. subtilis protein, suggesting that neither of these properties is functionally important. However, the mode of L-tryptophan binding and the proposed RNA binding surfaces are similar, indicating that both proteins are activated by l -tryptophan and bind RNA in essentially the same way. As expected, the TRAP:RNA complex from B. stearothermophilus is significantly more thermostable than that from B. subtilis, with optimal binding occurring at 70 degrees C.

  • Organizational Affiliation

    Department of Biological Sciences, State University of New York, Buffalo, NY, 14260, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K
74Geobacillus stearothermophilusMutation(s): 0 
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Explore Q9X6J6 
Go to UniProtKB:  Q9X6J6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X6J6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TRP

Download Ideal Coordinates CCD File 
L [auth A]
M [auth B]
N [auth C]
O [auth D]
P [auth E]
L [auth A],
M [auth B],
N [auth C],
O [auth D],
P [auth E],
Q [auth G],
R [auth G],
S [auth H],
T [auth I],
U [auth J],
V [auth K]
C11 H12 N2 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
TRP Binding MOAD:  1QAW Kd: 7500 (nM) from 1 assay(s)
PDBBind:  1QAW Kd: 7500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.93α = 90
b = 117.96β = 90
c = 147.63γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-04-16
    Type: Initial release
  • Version 1.1: 2007-10-21
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations, Structure summary