4AI5

Crystal structure of Y16F of 3-methyladenine DNA glycosylase I (TAG) in complex with 3-methyladenine

• PDB DOI: https://doi.org/10.2210/pdb4AI5/pdb

• Classification: HYDROLASE
• Organism(s): Staphylococcus aureus subsp. aureus MSSA476
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-02-08 Released: 2012-02-15 
• Deposition Author(s): Zhu, X., Naismith, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.216 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Literature

A Model for 3-Methyladenine Recognition by 3-Methyladenine DNA Glycosylase I (Tag) from Staphylococcus Aureus.

Zhu, X., Yan, X., Carter, L.G., Liu, H., Graham, S., Coote, P.J., Naismith, J.H.

(2012) Acta Crystallogr Sect F Struct Biol Cryst Commun 68: 610

• PubMed: 22684054 
• DOI: https://doi.org/10.1107/S1744309112016363
• Primary Citation of Related Structures:  
  4AI4, 4AI5, 4AIA


• PubMed Abstract: 
  

  The removal of chemically damaged DNA bases such as 3-methyladenine (3-MeA) is an essential process in all living organisms and is catalyzed by the enzyme 3-MeA DNA glycosylase I. A key question is how the enzyme selectively recognizes the alkylated 3-MeA over the much more abundant adenine. The crystal structures of native and Y16F-mutant 3-MeA DNA glycosylase I from Staphylococcus aureus in complex with 3-MeA are reported to 1.8 and 2.2 Å resolution, respectively. Isothermal titration calorimetry shows that protonation of 3-MeA decreases its binding affinity, confirming previous fluorescence studies that show that charge-charge recognition is not critical for the selection of 3-MeA over adenine. It is hypothesized that the hydrogen-bonding pattern of Glu38 and Tyr16 of 3-MeA DNA glycosylase I with a particular tautomer unique to 3-MeA contributes to recognition and selection.

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Organizational Affiliation: 

The BSRC, University of St Andrews, North Haugh, St Andrews KY16 9ST, Scotland.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors and generated by PISA (software)

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 5 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 109.24 kDa 
• Atom Count: 8,200 
• Modelled Residue Count: 936 
• Deposited Residue Count: 940 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-3-METHYLADENINE GLYCOSYLASE I	A, B, C, D, E	188	Staphylococcus aureus subsp. aureus MSSA476	Mutation(s): 1  EC: 3.2.2.20

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADK	G [auth A], J [auth B], M [auth C], P [auth D], R [auth E]	3-METHYL-3H-PURIN-6-YLAMINE C6 H7 N5 FSASIHFSFGAIJM-UHFFFAOYSA-N
SO4	H [auth A], K [auth B], N [auth C], S [auth E]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	F [auth A], I [auth B], L [auth C], O [auth D], Q [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
ADK	PDBBind:  4AI5	Kd: 1.20e+6 (nM) from 1 assay(s)
	Binding MOAD:  4AI5	Kd: 1.20e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.22 Å
• R-Value Free: 0.216 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.263	α = 90
b = 78.813	β = 90.53
c = 179.298	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Zhu, X., Naismith, J.H.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2012-06-13
  Changes: Other
• Version 1.2: 2012-06-20
  Changes: Other
• Version 1.3: 2018-04-04
  Changes: Data collection
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description