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:  
    1U8B, 1ZGW

  • 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 a mechanistic level ...

    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

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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Ada polyproteinE [auth A]133Escherichia coliMutation(s): 0 
Gene Names: ada
EC: 2.1.1 (UniProt), 2.1.1.63 (UniProt)
UniProt
Find proteins for P06134 (Escherichia coli (strain K12))
Explore P06134 
Go to UniProtKB:  P06134
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06134
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*TP*AP*AP*AP*TP*T)-3'A [auth B]6N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(P*AP*AP*TP*TP*T)-3'B [auth C]5N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(P*AP*AP*AP*GP*CP*GP*CP*AP*AP*GP*AP*T)-3'C [auth D]12N/A
Protein Feature View
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsLengthOrganismImage
5'-D(*AP*AP*TP*CP*TP*TP*GP*CP*GP*CP*TP*TP*T)-3'D [auth E]13N/A
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
F [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		E [auth A]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
SMC
Query on SMC		E [auth A]L-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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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