3G0Q

Crystal Structure of MutY bound to its inhibitor DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase.

Lee, S.Verdine, G.L.

(2009) Proc.Natl.Acad.Sci.Usa 106: 18497-18502

  • DOI: 10.1073/pnas.0902908106

  • PubMed Abstract: 
  • Adenine DNA glycosylase catalyzes the glycolytic removal of adenine from the promutagenic A.oxoG base pair in DNA. The general features of DNA recognition by an adenine DNA glycosylase, Bacillus stearothermophilus MutY, have previously been revealed ...

    Adenine DNA glycosylase catalyzes the glycolytic removal of adenine from the promutagenic A.oxoG base pair in DNA. The general features of DNA recognition by an adenine DNA glycosylase, Bacillus stearothermophilus MutY, have previously been revealed via the X-ray structure of a catalytically inactive mutant protein bound to an A:oxoG-containing DNA duplex. Although the structure revealed the substrate adenine to be, as expected, extruded from the DNA helix and inserted into an extrahelical active site pocket on the enzyme, the substrate adenine engaged in no direct contacts with active site residues. This feature was paradoxical, because other glycosylases have been observed to engage their substrates primarily through direct contacts. The lack of direct contacts in the case of MutY suggested that either MutY uses a distinctive logic for substrate recognition or that the X-ray structure had captured a noncatalytically competent state in lesion recognition. To gain further insight into this issue, we crystallized wild-type MutY bound to DNA containing a catalytically inactive analog of 2'-deoxyadenosine in which a single 2'-H atom was replaced by fluorine. The structure of this fluorinated lesion-recognition complex (FLRC) reveals the substrate adenine buried more deeply into the active site pocket than in the prior structure and now engaged in multiple direct hydrogen bonding and hydrophobic interactions. This structure appears to capture the catalytically competent state of adenine DNA glycosylases, and it suggests a catalytic mechanism for this class of enzymes, one in which general acid-catalyzed protonation of the nucleobase promotes glycosidic bond cleavage.


    Organizational Affiliation

    Departments of Stem Cell and Regenerative Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
A/G-specific adenine glycosylase
A
352Geobacillus stearothermophilusMutation(s): 2 
Gene Names: mutY
EC: 3.2.2.31
Find proteins for P83847 (Geobacillus stearothermophilus)
Go to UniProtKB:  P83847
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*AP*AP*GP*AP*CP*(8OG)P*GP*GP*GP*AP*C)-3'B11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*TP*CP*CP*CP*AP*GP*TP*CP*TP*T)-3'C11N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
8OG
Query on 8OG
B
DNA LINKINGC10 H14 N5 O8 PDG
A5L
Query on A5L
C
DNA LINKINGC10 H13 F N5 O6 PDA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.700α = 90.00
b = 85.900β = 90.00
c = 142.100γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
HKL-2000data reduction
DENZOdata reduction
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-01-28 
  • Released Date: 2009-11-17 
  • Deposition Author(s): Lee, S., Verdine, G.L.

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description
  • Version 1.3: 2018-01-24
    Type: Structure summary