6M3D

X-ray crystal structure of tandemly connected engrailed homeodomains (EHD) with R53A mutations and DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report



Literature

Structural basis for designing an array of engrailed homeodomains.

Sunami, T.Hirano, Y.Tamada, T.Kono, H.

(2020) Acta Crystallogr D Struct Biol 76: 824-833

  • DOI: 10.1107/S2059798320009237
  • Primary Citation of Related Structures:  
    6M3D

  • PubMed Abstract: 
  • Small DNA-binding proteins that target desired sequences have the potential to act as a scaffold for molecular tools such as genome editing. In this study, an engrailed homeodomain (EHD) was chosen and it was evaluated whether it could be used as a m ...

    Small DNA-binding proteins that target desired sequences have the potential to act as a scaffold for molecular tools such as genome editing. In this study, an engrailed homeodomain (EHD) was chosen and it was evaluated whether it could be used as a molecular module that can connect to itself to recognize a longer target sequence. It was previously shown that two EHDs connected by a linker (EHD 2 ) recognize a target sequence twice as long as that recognized by a single EHD in cells only when Arg53 in each EHD in the tandem protein is mutated to alanine {(EHD[R53A]) 2 }. To investigate the recognition mechanism of (EHD[R53A]) 2 , the crystal structure of the (EHD[R53A]) 2 -DNA complex was determined at 1.6 Å resolution. The individual EHDs were found to adopt the typical homeodomain fold. Most importantly, the base-specific interactions in the major groove necessary for the affinity/specificity of wild-type EHD were preserved in (EHD[R53A]) 2 . Bacterial assays confirmed that the base-specific interactions are retained under cellular conditions. These observations indicate that the R53A mutation only causes a loss of the arginine-phosphate interaction at the protein-DNA interface, which reduces the DNA-binding affinity compared with the wild type. It is therefore concluded that (EHD[R53A]) 2 precisely recognizes tandem target sites within cells, enabling the individual EHDs to concurrently bind to the target sites with modest binding affinity. This suggests that modulation of the binding activity of each EHD is vital to construct a protein array that can precisely recognize a sequence with multiple target sites.


    Organizational Affiliation

    Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa 619-0215, Japans.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Segmentation polarity homeobox protein engrailed,Segmentation polarity homeobox protein engrailedC148Drosophila melanogasterMutation(s): 4 
Gene Names: enCG9015
Find proteins for P02836 (Drosophila melanogaster)
Explore P02836 
Go to UniProtKB:  P02836
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*TP*AP*AP*TP*CP*CP*TP*AP*AP*TP*CP*C)-3')A12synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*GP*AP*TP*TP*AP*GP*GP*AP*TP*TP*A)-3')B12synthetic construct
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      NA
      Query on NA

      Download CCD File 
      A
      SODIUM ION
      Na
      FKNQFGJONOIPTF-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.60 Å
      • R-Value Free: 0.236 
      • R-Value Work: 0.188 
      • R-Value Observed: 0.191 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 39.798α = 90
      b = 61.437β = 106.447
      c = 39.976γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XDSdata reduction
      Aimlessdata scaling
      PHASERphasing

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Japan Society for the Promotion of Science (JSPS)Japan26840054
      Japan Society for the Promotion of Science (JSPS)Japan26330339
      Japan Society for the Promotion of Science (JSPS)JapanJP18H05534

      Revision History 

      • Version 1.0: 2020-09-16
        Type: Initial release