1T38

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.307 
  • R-Value Work: 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:  

  • 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 ...

    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: 
    • 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
    • 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


    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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Methylated-DNA--protein-cysteine methyltransferase
A
188Homo sapiensMutation(s): 1 
Gene Names: MGMT
EC: 2.1.1.63
Find proteins for P16455 (Homo sapiens)
Go to Gene View: MGMT
Go to UniProtKB:  P16455
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*CP*AP*TP*GP*(6OG)P*CP*TP*AP*GP*TP*A)-3'B13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3'C13N/A
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
6OG
Query on 6OG
B
DNA LINKINGC11 H16 N5 O7 PDG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.261 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 115.698α = 90.00
b = 115.698β = 90.00
c = 106.775γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
AMoREphasing
MOSFLMdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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