3ZQC

Structure of the Trichomonas vaginalis Myb3 DNA-binding domain bound to a promoter sequence reveals a unique C-terminal beta-hairpin conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


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Literature

Structure of the Trichomonas Vaginalis Myb3 DNA-Binding Domain Bound to a Promoter Sequence Reveals a Unique C-Terminal Beta-Hairpin Conformation.

Wei, S.-Y.Lou, Y.-C.Tsai, J.-Y.Ho, M.R.Chou, C.C.Rajasekaran, M.Hsu, H.-M.Tai, J.-H.Hsiao, C.-D.Chen, C.

(2012) Nucleic Acids Res. 40: 449

  • DOI: 10.1093/nar/gkr707

  • PubMed Abstract: 
  • Trichomonas vaginalis Myb3 transcription factor (tvMyb3) recognizes the MRE-1 promoter sequence and regulates ap65-1 gene, which encodes a hydrogenosomal malic enzyme that may play a role in the cytoadherence of the parasite. Here, we identified tvMy ...

    Trichomonas vaginalis Myb3 transcription factor (tvMyb3) recognizes the MRE-1 promoter sequence and regulates ap65-1 gene, which encodes a hydrogenosomal malic enzyme that may play a role in the cytoadherence of the parasite. Here, we identified tvMyb3(53-180) as the essential fragment for DNA recognition and report the crystal structure of tvMyb3(53-180) bound to MRE-1 DNA. The N-terminal fragment adopts the classical conformation of an Myb DNA-binding domain, with the third helices of R2 and R3 motifs intercalating in the major groove of DNA. The C-terminal extension forms a β-hairpin followed by a flexible tail, which is stabilized by several interactions with the R3 motif and is not observed in other Myb proteins. Interestingly, this unique C-terminal fragment does not stably connect with DNA in the complex structure but is involved in DNA binding, as demonstrated by NMR chemical shift perturbation, (1)H-(15)N heteronuclear-nuclear Overhauser effect and intermolecular paramagnetic relaxation enhancement. Site-directed mutagenesis also revealed that this C-terminal fragment is crucial for DNA binding, especially the residue Arg(153) and the fragment K(170)KRK(173). We provide a structural basis for MRE-1 DNA recognition and suggest a possible post-translational regulation of tvMyb3 protein.


    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan, ROC.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
MYB3
A, D, G, J
131Trichomonas vaginalisMutation(s): 0 
Find proteins for A2D9X4 (Trichomonas vaginalis)
Go to UniProtKB:  A2D9X4
Entity ID: 2
MoleculeChainsLengthOrganism
MRE-1B,E,H,K16Trichomonas vaginalis
Entity ID: 3
MoleculeChainsLengthOrganism
MRE-1C,F,I,L16Trichomonas vaginalis
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.218 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.810α = 94.68
b = 71.770β = 97.84
c = 87.820γ = 99.28
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-04-18
    Type: Initial release