1T38

HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE BOUND TO DNA CONTAINING O6-METHYLGUANINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.261 
  • R-Value Observed: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

DNA binding and nucleotide flipping by the human DNA repair protein AGT.

Daniels, D.S.Woo, T.T.Luu, K.X.Noll, D.M.Clarke, N.D.Pegg, A.E.Tainer, J.A.

(2004) Nat Struct Mol Biol 11: 714-720

  • DOI: 10.1038/nsmb791
  • Primary Citation of Related Structures:  
    1T39, 1T38

  • PubMed Abstract: 
  • O(6)-alkylguanine-DNA alkyltransferase (AGT), or O(6)-methylguanine-DNA methyltransferase (MGMT), prevents mutations and apoptosis resulting from alkylation damage to guanines. AGT irreversibly transfers the alkyl lesion to an active site cysteine in a stoichiometric, direct damage reversal pathway ...

    O(6)-alkylguanine-DNA alkyltransferase (AGT), or O(6)-methylguanine-DNA methyltransferase (MGMT), prevents mutations and apoptosis resulting from alkylation damage to guanines. AGT irreversibly transfers the alkyl lesion to an active site cysteine in a stoichiometric, direct damage reversal pathway. AGT expression therefore elicits tumor resistance to alkylating chemotherapies, and AGT inhibitors are in clinical trials. We report here structures of human AGT in complex with double-stranded DNA containing the biological substrate O(6)-methylguanine or crosslinked to the mechanistic inhibitor N(1),O(6)-ethanoxanthosine. The prototypical DNA major groove-binding helix-turn-helix (HTH) motif mediates unprecedented minor groove DNA binding. This binding architecture has advantages for DNA repair and nucleotide flipping, and provides a paradigm for HTH interactions in sequence-independent DNA-binding proteins like RecQ and BRCA2. Structural and biochemical results further support an unpredicted role for Tyr114 in nucleotide flipping through phosphate rotation and an efficient kinetic mechanism for locating alkylated bases.


    Related Citations: 
    • Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding
      Daniels, D.S., Mol, C.D., Arvai, A.S., Kanugula, S., Pegg, A.E., Tainer, J.A.
      (2000) EMBO J 19: 1719
    • Conserved structural motifs governing the stoichiometric repair of alkylated DNA by O(6)-alkylguanine-DNA alkyltransferase
      Daniels, D.S., Tainer, J.A.
      (2000) Mutat Res 460: 151

    Organizational Affiliation

    Skaggs Institute for Chemical Biology, The Scripps Research Institute, MB-4, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Methylated-DNA--protein-cysteine methyltransferaseC [auth A]188Homo sapiensMutation(s): 1 
Gene Names: MGMT
EC: 2.1.1.63
UniProt & NIH Common Fund Data Resources
Find proteins for P16455 (Homo sapiens)
Explore P16455 
Go to UniProtKB:  P16455
PHAROS:  P16455
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3'A [auth B]13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3'B [auth C]13N/A
      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: 0.307 
      • R-Value Work: 0.261 
      • R-Value Observed: 0.261 
      • Space Group: I 41 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 115.698α = 90
      b = 115.698β = 90
      c = 106.775γ = 90
      Software Package:
      Software NamePurpose
      CNSrefinement
      MOSFLMdata reduction
      CCP4data scaling
      AMoREphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2004-07-13
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance