1F4R

CRYSTAL STRUCTURE OF THE HUMAN AAG DNA REPAIR GLYCOSYLASE COMPLEXED WITH 1,N6-ETHENOADENINE-DNA

• PDB DOI: https://doi.org/10.2210/pdb1F4R/pdb
• NAKB: 1F4R

• Classification: HYDROLASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-06-08 Released: 2000-12-11 
• Deposition Author(s): Lau, A.Y., Wyatt, M.D., Glassner, B.J., Samson, L.D., Ellenberger, T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.276 
• R-Value Work: 0.239 

Literature

Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG.

Lau, A.Y., Wyatt, M.D., Glassner, B.J., Samson, L.D., Ellenberger, T.

(2000) Proc Natl Acad Sci U S A 97: 13573-13578

• PubMed: 11106395 
• DOI: https://doi.org/10.1073/pnas.97.25.13573
• Primary Citation of Related Structures:  
  1EWN, 1F4R, 1F6O


• PubMed Abstract: 
  

  The human 3-methyladenine DNA glycosylase [alkyladenine DNA glycosylase (AAG)] catalyzes the first step of base excision repair by cleaving damaged bases from DNA. Unlike other DNA glycosylases that are specific for a particular type of damaged base, AAG excises a chemically diverse selection of substrate bases damaged by alkylation or deamination. The 2.1-A crystal structure of AAG complexed to DNA containing 1,N(6)-ethenoadenine suggests how modified bases can be distinguished from normal DNA bases in the enzyme active site. Mutational analyses of residues contacting the alkylated base in the crystal structures suggest that the shape of the damaged base, its hydrogen-bonding characteristics, and its aromaticity all contribute to the selective recognition of damage by AAG.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.32 kDa 
• Atom Count: 2,064 
• Modelled Residue Count: 223 
• Deposited Residue Count: 245 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
3-METHYL-ADENINE DNA GLYCOSYLASE	C [auth A]	219	Homo sapiens	Mutation(s): 0  EC: 3.2.2.20 (PDB Primary Data), 3.2.2.21 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P29372 (Homo sapiens) Explore P29372  Go to UniProtKB:  P29372
PHAROS:  P29372 GTEx:  ENSG00000103152

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*CP*AP*TP*GP*(EDA)P*TP*TP*GP*CP*CP*T)-3')	A [auth D]	13	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3')	B [auth E]	13	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.276 
• R-Value Work: 0.239 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.1	α = 90
b = 57.3	β = 90
c = 125.5	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-12-11 
Deposition Author(s): Lau, A.Y., Wyatt, M.D., Glassner, B.J., Samson, L.D., Ellenberger, T.

Revision History  

• Version 1.0: 2000-12-11
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations