1T39

HUMAN O6-ALKYLGUANINE-DNA ALKYLTRANSFERASE COVALENTLY CROSSLINKED TO DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.296 

Starting Model: experimental
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This is version 1.3 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: https://doi.org/10.1038/nsmb791
  • Primary Citation of Related Structures:  
    1T38, 1T39

  • 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. 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Methylated-DNA--protein-cysteine methyltransferaseE [auth A],
F [auth B]
188Homo sapiensMutation(s): 0 
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
GTEx:  ENSG00000170430 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16455
Sequence Annotations
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  • Reference Sequence

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Entity ID: 1
MoleculeChains LengthOrganismImage
5'-D(*GP*CP*CP*AP*TP*GP*(E1X)P*CP*TP*AP*GP*TP*A)-3'A [auth C],
C [auth E]
13N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*TP*AP*CP*TP*AP*GP*CP*CP*AP*TP*GP*GP*C)-3'B [auth D],
D [auth F]
13N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 0.344 
  • R-Value Work: 0.296 
  • R-Value Observed: 0.296 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.145α = 90
b = 41.25β = 103.14
c = 70.629γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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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
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description