3BVS | pdb_00003bvs

Crystal Structure of Bacillus cereus Alkylpurine DNA Glycosylase AlkD

• PDB DOI: https://doi.org/10.2210/pdb3BVS/pdb

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


• Deposited: 2008-01-07 Released: 2008-07-15 
• Deposition Author(s): Rubinson, E.H., Eichman, B.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

A New Protein Architecture for Processing Alkylation Damaged DNA: The Crystal Structure of DNA Glycosylase AlkD.

Rubinson, E.H., Metz, A.H., O'Quin, J., Eichman, B.F.

(2008) J Mol Biology 381: 13-23

• PubMed: 18585735 
• DOI: https://doi.org/10.1016/j.jmb.2008.05.078
• Primary Citation Related Structures: 
  3BVS


• PubMed Abstract: 
  

  DNA glycosylases safeguard the genome by locating and excising chemically modified bases from DNA. AlkD is a recently discovered bacterial DNA glycosylase that removes positively charged methylpurines from DNA, and was predicted to adopt a protein fold distinct from from those of other DNA repair proteins. The crystal structure of Bacillus cereus AlkD presented here shows that the protein is composed exclusively of helical HEAT-like repeats, which form a solenoid perfectly shaped to accommodate a DNA duplex on the concave surface. Structural analysis of the variant HEAT repeats in AlkD provides a rationale for how this protein scaffolding motif has been modified to bind DNA. We report 7mG excision and DNA binding activities of AlkD mutants, along with a comparison of alkylpurine DNA glycosylase structures. Together, these data provide important insight into the requirements for alkylation repair within DNA and suggest that AlkD utilizes a novel strategy to manipulate DNA in its search for alkylpurine bases.

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Organizational Affiliation: 
• Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 28.42 kDa 
• Atom Count: 1,974 
• Modeled Residue Count: 227 
• Deposited Residue Count: 239 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alkylpurine DNA Glycosylase AlkD	A	239	Bacillus cereus	Mutation(s): 0  Gene Names: AlkD
UniProt
Find proteins for Q816E8 (Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)) Explore Q816E8  Go to UniProtKB:  Q816E8

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.227 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.917	α = 90
b = 77.917	β = 90
c = 55.102	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-07-15 
Deposition Author(s): Rubinson, E.H., Eichman, B.F.

Revision History  

• Version 1.0: 2008-07-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references