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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.jmb.2005.05.028

  • 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 doubl ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Methylated-DNA--protein-cysteine methyltransferase
A, B, C
179Homo sapiensMutation(s): 0 
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*TP*GP*GP*AP*TP*GP*(XCY)P*GP*TP*GP*TP*AP*GP*GP*T)-3'D,F16N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*CP*TP*AP*CP*AP*CP*AP*CP*AP*TP*CP*CP*AP*CP*A)-3'E,G16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
XCY
Query on XCY
D, F
DNA LINKINGC17 H23 N4 O7 PDC
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.246 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 58.150α = 90.00
b = 102.710β = 106.77
c = 87.940γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance