1QAW

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1006/jmbi.1999.2834

  • 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 str ...

    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.


    Related Citations: 
    • The Structure of Trp RNA-Binding Attenuation Protein
      Antson, A.A.,Otridge, J.,Brzozowski, A.M.,Dodson, E.J.,Dodson, G.G.,Wilson, K.S.,Smith, T.M.,Yang, M.,Kurecki, T.,Gollnick, P.
      (1995) Nature 374: 693
    • 11-Fold Symmetry of the Trp RNA-Binding Attenuation Protein (Trap)from Bacillus Subtilis Determined by X-Ray Analysis
      Antson, A.A.,Brzozowski, A.M.,Dodson, E.J.,Dauter, Z.,Wilson, K.S.,Kurecki, T.,Otridge, J.,Gollnick, P.
      (1994) J.Mol.Biol. 244: 1


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRP RNA-BINDING ATTENUATION PROTEIN
A, B, C, D, E, F, G, H, I, J, K
74Geobacillus stearothermophilusMutation(s): 0 
Gene Names: mtrB
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9X6J6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download SDF File 
Download CCD File 
A, B, C, D, E, G, H, I, J, K
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TRPKd: 7500 nM BINDINGMOAD
TRPKd: 7500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 65.930α = 90.00
b = 117.960β = 90.00
c = 147.630γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-04-16
    Type: Initial release
  • Version 1.1: 2007-10-21
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance