2ZP9

The Nature of the TRAP:Anti-TRAP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 

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This is version 1.2 of the entry. See complete history


Literature

The nature of the TRAP-Anti-TRAP complex.

Watanabe, M.Heddle, J.G.Kikuchi, K.Unzai, S.Akashi, S.Park, S.Y.Tame, J.R.

(2009) Proc Natl Acad Sci U S A 106: 2176-2181

  • DOI: 10.1073/pnas.0801032106
  • Primary Citation of Related Structures:  
    2ZP8, 2ZP9

  • PubMed Abstract: 
  • Tryptophan biosynthesis is subject to exquisite control in species of Bacillus and has become one of the best-studied model systems in gene regulation. The protein TRAP (trp RNA-binding attenuation protein) predominantly forms a ring-shaped 11-mer, which binds cognate RNA in the presence of tryptophan to suppress expression of the trp operon ...

    Tryptophan biosynthesis is subject to exquisite control in species of Bacillus and has become one of the best-studied model systems in gene regulation. The protein TRAP (trp RNA-binding attenuation protein) predominantly forms a ring-shaped 11-mer, which binds cognate RNA in the presence of tryptophan to suppress expression of the trp operon. TRAP is itself regulated by the protein Anti-TRAP, which binds to TRAP and prevents RNA binding. To date, the nature of this interaction has proved elusive. Here, we describe mass spectrometry and analytical centrifugation studies of the complex, and 2 crystal structures of the TRAP-Anti-TRAP complex. These crystal structures, both refined to 3.2-A resolution, show that Anti-TRAP binds to TRAP as a trimer, sterically blocking RNA binding. Mass spectrometry shows that 11-mer TRAP may bind up to 5 AT trimers, and an artificial 12-mer TRAP may bind 6. Both forms of TRAP make the same interactions with Anti-TRAP. Crystallization of wild-type TRAP with Anti-TRAP selectively pulls the 12-mer TRAP form out of solution, so the crystal structure of wild-type TRAP-Anti-TRAP complex reflects a minor species from a mixed population.


    Organizational Affiliation

    Yokohama City University, Tsurumi, Suehiro 1-7-29, Yokohama 230-0045, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription attenuation protein mtrBA, B, F, G, K, L81Geobacillus stearothermophilusMutation(s): 0 
Gene Names: mtrB
UniProt
Find proteins for Q9X6J6 (Geobacillus stearothermophilus)
Explore Q9X6J6 
Go to UniProtKB:  Q9X6J6
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tryptophan RNA-binding attenuator protein-inhibitory protein
C, D, E, H, I, J, M, N
C, D, E, H, I, J, M, N, O
53Bacillus subtilisMutation(s): 0 
Gene Names: rtpAyczABSU02530
UniProt
Find proteins for O31466 (Bacillus subtilis (strain 168))
Explore O31466 
Go to UniProtKB:  O31466
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.325 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 197.134α = 90
b = 197.135β = 90
c = 56.658γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-03
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2014-03-05
    Changes: Database references