1U8B

Crystal structure of the methylated N-ADA/DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.274 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.235 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A methylation-dependent electrostatic switch controls DNA repair and transcriptional activation by E. coli ada.

He, C.Hus, J.C.Sun, L.J.Zhou, P.Norman, D.P.Dotsch, V.Wei, H.Gross, J.D.Lane, W.S.Wagner, G.Verdine, G.L.

(2005) Mol Cell 20: 117-129

  • DOI: 10.1016/j.molcel.2005.08.013
  • Primary Citation of Related Structures:  
    1ZGW, 1U8B

  • PubMed Abstract: 
  • The transcriptional activity of many sequence-specific DNA binding proteins is directly regulated by posttranslational covalent modification. Although this form of regulation was first described nearly two decades ago, it remains poorly understood at ...

    The transcriptional activity of many sequence-specific DNA binding proteins is directly regulated by posttranslational covalent modification. Although this form of regulation was first described nearly two decades ago, it remains poorly understood at a mechanistic level. The prototype for a transcription factor controlled by posttranslational modification is E. coli Ada protein, a chemosensor that both repairs methylation damage in DNA and coordinates the resistance response to genotoxic methylating agents. Ada repairs methyl phosphotriester lesions in DNA by transferring the aberrant methyl group to one of its own cysteine residues; this site-specific methylation enhances tremendously the DNA binding activity of the protein, thereby enabling it to activate a methylation-resistance regulon. Here, we report solution and X-ray structures of the Cys-methylated chemosensor domain of Ada bound to DNA. The structures reveal that both phosphotriester repair and methylation-dependent transcriptional activation function through a zinc- and methylation-dependent electrostatic switch.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ada polyproteinA133Escherichia coliMutation(s): 0 
Gene Names: ada
EC: 2.1.1 (UniProt), 2.1.1.63 (UniProt)
Find proteins for P06134 (Escherichia coli (strain K12))
Explore P06134 
Go to UniProtKB:  P06134
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*TP*AP*AP*AP*TP*T)-3'B6N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(P*AP*AP*TP*TP*T)-3'C5N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 3
        MoleculeChainsLengthOrganismImage
        5'-D(P*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*AP*T)-3'D12N/A
        • Find similar nucleic acids by:  Sequence   |   Structure
        • Entity ID: 4
          MoleculeChainsLengthOrganismImage
          5'-D(*AP*AP*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*T)-3'E13N/A
          Small Molecules
          Ligands 1 Unique
          IDChainsName / Formula / InChI Key2D Diagram3D Interactions
          ZN
          Query on ZN

          Download CCD File 
          A
          ZINC ION
          Zn
          PTFCDOFLOPIGGS-UHFFFAOYSA-N
           Ligand Interaction
          Modified Residues  2 Unique
          IDChainsTypeFormula2D DiagramParent
          MSE
          Query on MSE
          AL-PEPTIDE LINKINGC5 H11 N O2 SeMET
          SMC
          Query on SMC
          AL-PEPTIDE LINKINGC4 H9 N O2 SCYS
          Experimental Data & Validation

          Experimental Data

          • Method: X-RAY DIFFRACTION
          • Resolution: 2.10 Å
          • R-Value Free: 0.274 
          • R-Value Work: 0.235 
          • R-Value Observed: 0.235 
          • Space Group: P 21 21 21
          Unit Cell:
          Length ( Å )Angle ( ˚ )
          a = 28.842α = 90
          b = 84.593β = 90
          c = 108.357γ = 90
          Software Package:
          Software NamePurpose
          DENZOdata reduction
          SCALEPACKdata scaling
          CNSrefinement
          CNSphasing

          Structure Validation

          View Full Validation Report



          Entry History 

          Deposition Data

          Revision History 

          • Version 1.0: 2005-10-11
            Type: Initial release
          • Version 1.1: 2008-04-30
            Changes: Version format compliance
          • Version 1.2: 2011-07-13
            Changes: Version format compliance