1GTN

Structure of the trp RNA-binding attenuation protein (TRAP) bound to an RNA molecule containing 11 GAGCC repeats


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Specificity of Trap-RNA Interactions: Crystal Structures of Two Complexes with Different RNA Sequences

Hopcroft, N.H.Wendt, A.L.Gollnick, P.Antson, A.A.

(2002) Acta Crystallogr.,Sect.D 58: 615

  • Primary Citation of Related Structures:  1GTF
  • Also Cited By: 1UTD, 1UTF, 1UTV, 4V4F, 5EEU, 5EEV, 5EEX, 5EEY, 5EEZ, 5EF0, 5EF1, 5EF2, 5EF3

  • PubMed Abstract: 
  • The trp RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in bacilli by binding to the leader region of the nascent trp operon mRNA. When activated by binding tryptophan, the 11-subunit circular TRAP mol ...

    The trp RNA-binding attenuation protein (TRAP) regulates expression of the tryptophan biosynthetic genes in bacilli by binding to the leader region of the nascent trp operon mRNA. When activated by binding tryptophan, the 11-subunit circular TRAP molecule binds to a target sequence consisting of 11 (G/U)AG repeats, separated by two or three variable 'spacer' nucleotides. Reported here are two crystal structures of TRAP bound to RNAs containing 11 GAG repeats separated by UU and CC spacer nucleotides, determined at 1.75 and 2.50 A resolution, respectively. These show the spacer regions of the RNA molecules to be highly flexible, making no direct hydrogen-bonding contacts with the protein. Comparison of these structures with the previous structure of TRAP bound to (GAGAU)(10)GAG RNA, in which the spacer nucleotides stack with each other close to the protein surface, shows that the RNA can adopt different conformations depending on the sequence of the spacer regions. This gives insight into the structural basis of the specificity of TRAP and into the mechanism of binding.


    Related Citations: 
    • Structure of the Trp RNA-Binding Attenuation Protein, Trap, Bound to RNA
      Antson, A.A.,Dodson, E.J.,Dodson, G.G.,Greaves, R.B.,Chen, X.,Gollnick, P.
      (1999) Nature 401: 235


    Organizational Affiliation

    York Structural Biology Laboratory, Department of Chemistry, University of York, York Y010 5DD, England.




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, L, M, N, O, P, Q, R, S, T, U, V
74Geobacillus stearothermophilusGene Names: mtrB
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Go to UniProtKB:  Q9X6J6
Entity ID: 2
MoleculeChainsLengthOrganism
(GAGCC)11G 56-NUCLEOTIDE RNAW56N/A
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, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.235 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 145.839α = 90.00
b = 111.722β = 117.78
c = 138.715γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance