8DWE | pdb_00008dwe

Adenine glycosylase MutY variant E43Q in complex with DNA containing d(8-oxo-G) paired with substrate purine

• PDB DOI: https://doi.org/10.2210/pdb8DWE/pdb
• NAKB: 8DWE

• Classification: HYDROLASE/DNA
• Organism(s): Geobacillus stearothermophilus, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-08-01 Released: 2023-08-09 
• Deposition Author(s): Russelburg, L.P., Demir, M., David, S.S., Horvath, M.P.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for Nucleobase Activation by the Adenine DNA Glycosylase MutY.

Russelburg, L.P., Demir, M., Cedeno, K., David, S.S., Horvath, M.P.

(2026) Chembiochem 27: e70414-e70414

• PubMed: 42281263 
• DOI: https://doi.org/10.1002/cbic.70414
• Primary Citation Related Structures: 
  8DWD, 8DWE, 8DWF


• PubMed Abstract: 
  

  The DNA glycosylase MutY excises adenine when mispaired with oxidized guanine (OG). While it is understood that inappropriate adenine excision would be catastrophic, the mechanism by which MutY activity is kept in check and only licensed at OG:A lesions is unknown. To explore the structural basis for nucleobase activation, we tested kinetic and structural consequences following replacement of the catalytic Glu, a signature residue for MutY. E43Q and E43S substitution variants of MutY from Geobacillus stearothermophilus, though severely impaired, retained measurable activity. X-ray crystal structures showed the substrate nucleobase in an anti conformation, rotated by 180° from the syn conformation seen in previous substrate complexes. Remarkably, the AP product was observed as the alpha-anomer configuration when generated by these Glu-replacement variants, completely different from the beta-anomer AP product expected for the wild-type enzyme and seen directly for other cancer-associated variants. Our results suggest a mechanism for regulating MutY, whereby Glu engagement with the syn conformation of the nucleobase licenses a "go ahead" state for adenine excision only at OG:A lesions, while Glu dis-engagement establishes an "on hold" state to avoid inappropriate activity elsewhere.

---

Organizational Affiliation: 
• School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA.
Department of Chemistry, Chemistry and Chemical Biology Graduate Program, University of California DavisOne Shields AvenueDavis, California, USA.

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

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

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 98.24 kDa 
• Atom Count: 6,611 
• Modeled Residue Count: 751 
• Deposited Residue Count: 774 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenine DNA glycosylase	A, D	365	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: mutY EC: 3.2.2.31
UniProt
Find proteins for P83847 (Geobacillus stearothermophilus) Explore P83847  Go to UniProtKB:  P83847

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*GP*AP*CP*(8OG)P*TP*GP*GP*AP*C)-3')	B, E	11	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*GP*TP*CP*CP*AP*(PRN)P*GP*TP*CP*T)-3')	C, F	11	synthetic construct

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4 (Subject of Investigation/LOI)	G [auth A], L [auth D]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
TRS	K [auth B], P [auth E]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
EDO	H [auth A], M [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	I [auth A], J [auth A], N [auth D], O [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.234 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.63	α = 90
b = 137.96	β = 101
c = 74.49	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-08-09 
Deposition Author(s): Russelburg, L.P., Demir, M., David, S.S., Horvath, M.P.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1905304
National Science Foundation (NSF, United States)	United States	1905249
National Science Foundation (NSF, United States)	United States	1610721
National Science Foundation (NSF, United States)	United States	1608934

Revision History  

• Version 1.0: 2023-08-09
  Type: Initial release
  
• Version 1.1: 2024-05-22
  Changes: Data collection
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary
• Version 1.3: 2026-06-03
  Changes: Database references
• Version 1.4: 2026-08-12
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Derived calculations, Structure summary
• Version 1.5: 2026-09-09
  Changes: Database references