1YFH

wt Human O6-Alkylguanine-DNA Alkyltransferase Bound To DNA Containing an Alkylated Cytosine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The structure of the human AGT protein bound to DNA and its implications for damage detection.

Duguid, E.M.Rice, P.A.He, C.

(2005) J Mol Biol 350: 657-666

  • DOI: https://doi.org/10.1016/j.jmb.2005.05.028
  • Primary Citation of Related Structures:  
    1YFH

  • PubMed Abstract: 

    O6-Alklyguanine-DNA alkyltransferase (AGT) is an important DNA repair protein that protects cells from mutagenesis and toxicity arising from alkylating agents. We present an X-ray crystal structure of the wild-type human protein (hAGT) bound to double-stranded DNA with a chemically modified cytosine base. The protein binds at two different sites: one at the modified base, and the other across a sticky-ended DNA junction. The protein molecule that binds the modified cytosine base flips the base and recognizes it in its active site. The one that binds ends of neighboring DNA molecules partially flips an overhanging thymine base. This base is not inserted into the active-site pocket of the protein. These two different hAGT/DNA interactions observed in the structure suggest that hAGT may not detect DNA lesions by searching for the adduct itself, but rather for weakened and/or distorted base-pairs caused by base damage in the duplex DNA. We propose that hAGT imposes a strain on the DNA duplex and searches for DNA regions where the native structure is destabilized. The structure provides implications for pyrimidine recognition, improved inhibitor design, and a possible protein/protein interaction patch on hAGT.


  • Organizational Affiliation

    Department of Chemistry, 5735 South Ellis Avenue, The University of Chicago, Chicago, IL 60637, USA.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Methylated-DNA--protein-cysteine methyltransferaseE [auth A],
F [auth B],
G [auth C]
179Homo 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*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-3'A [auth D],
C [auth F]
16N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3'B [auth E],
D [auth G]
16N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.15α = 90
b = 102.71β = 106.77
c = 87.94γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-13
    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