1PVS

3-methyladenine Glcosylase II(AlkA) Hypoxanthine complex

• PDB DOI: https://doi.org/10.2210/pdb1PVS/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-06-28 Released: 2004-06-08 
• Deposition Author(s): Teale, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.292 
• R-Value Work: 0.232 

Literature

3-methyladenine-DNA glycosylase II: the crystal structure of an AlkA-hypoxanthine complex suggests the possibility of product inhibition.

Teale, M., Symersky, J., DeLucas, L.

(2002) Bioconjug Chem 13: 403-407

• PubMed: 12009927 
• DOI: https://doi.org/10.1021/bc015527v
• Primary Citation of Related Structures:  
  1PVS


• PubMed Abstract: 
  

  Escherichia coli (E. coli) protein 3-methyladenine-DNA glycosylase II (AlkA) functions primarily by removing alkylation damage from duplex and single stranded DNA. A crystal structure of AlkA was refined to 2.0 A resolution. This structure in turn was used to refine an AlkA-hypoxanthine (substrate) complex structure to 2.4 A resolution. The complex structure shows hypoxanthine located in AlkA's active site stacked between residues W218 and Y239. The structural analysis of the AlkA and AlkA-hypoxanthine structures indicate that free hypoxanthine binding in the active site may inhibit glycosylase activity.

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Organizational Affiliation: 

Laboratory for Structural Biology, University of Alabama in Huntsville, 35899, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 63.12 kDa 
• Atom Count: 4,676 
• Modelled Residue Count: 564 
• Deposited Residue Count: 564 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-3-methyladenine glycosylase II	A, B	282	Escherichia coli	Mutation(s): 0  Gene Names: ALKA OR AIDA OR B2068 EC: 3.2.2.21
UniProt
Find proteins for P04395 (Escherichia coli (strain K12)) Explore P04395  Go to UniProtKB:  P04395

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7HP	C [auth A], D [auth B]	7-HYDROXY-PYRAZOLO[4,3-D]PYRIMIDINE C5 H4 N4 O JFZSDNLQDTYVEE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.292 
• R-Value Work: 0.232 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.005	α = 90
b = 75.979	β = 110.03
c = 61.417	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-08 
Deposition Author(s): Teale, M.

Revision History  

• Version 1.0: 2004-06-08
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations