5CL5

Alkylpurine DNA glycosylase AlkD bound to DNA containing a 3-methyladenine analog or DNA containing an abasic site and a free nucleobase (51% substrate/49% product at 48 hours)

• PDB DOI:  https://doi.org/10.2210/pdb5CL5/pdb
• NAKB: 5CL5

• Classification: HYDROLASE/DNA
• Organism(s): Bacillus cereus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-16 Released: 2015-10-28 
• Deposition Author(s): Mullins, E.A., Eichman, B.F.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.189 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

Literature

The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.

Mullins, E.A., Shi, R., Parsons, Z.D., Yuen, P.K., David, S.S., Igarashi, Y., Eichman, B.F.

(2015) Nature 527: 254-258

• PubMed: 26524531 
• DOI: https://doi.org/10.1038/nature15728
• Primary Citation of Related Structures:  
  5CL3, 5CL4, 5CL5, 5CL6, 5CL7, 5CL8, 5CL9, 5CLA, 5CLB, 5CLC, 5CLD, 5CLE


• PubMed Abstract: 
  

Threats to genomic integrity arising from DNA damage are mitigated by DNA glycosylases, which initiate the base excision repair pathway by locating and excising aberrant nucleobases. How these enzymes find small modifications within the genome is a current area of intensive research. A hallmark of these and other DNA repair enzymes is their use of base flipping to sequester modified nucleotides from the DNA helix and into an active site pocket. Consequently, base flipping is generally regarded as an essential aspect of lesion recognition and a necessary precursor to base excision. Here we present the first, to our knowledge, DNA glycosylase mechanism that does not require base flipping for either binding or catalysis. Using the DNA glycosylase AlkD from Bacillus cereus, we crystallographically monitored excision of an alkylpurine substrate as a function of time, and reconstructed the steps along the reaction coordinate through structures representing substrate, intermediate and product complexes. Instead of directly interacting with the damaged nucleobase, AlkD recognizes aberrant base pairs through interactions with the phosphoribose backbone, while the lesion remains stacked in the DNA duplex. Quantum mechanical calculations revealed that these contacts include catalytic charge-dipole and CH-π interactions that preferentially stabilize the transition state. We show in vitro and in vivo how this unique means of recognition and catalysis enables AlkD to repair large adducts formed by yatakemycin, a member of the duocarmycin family of antimicrobial natural products exploited in bacterial warfare and chemotherapeutic trials. Bulky adducts of this or any type are not excised by DNA glycosylases that use a traditional base-flipping mechanism. Hence, these findings represent a new model for DNA repair and provide insights into catalysis of base excision.

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Organizational Affiliation: 

Department of Biological Sciences and Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 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: 36.07 kDa 
• Atom Count: 2,875 
• Modelled Residue Count: 256 
• Deposited Residue Count: 266 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AlkD	A	241	Bacillus cereus	Mutation(s): 0  Gene Names: IKE_03968 EC: 3.2.2
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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*CP*GP*AP*(DZM)P*AP*GP*TP*CP*CP*G)-3')	B	12	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*GP*AP*CP*TP*TP*TP*CP*GP*GP*G)-3')	C	12	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
54K	D [auth B]	7-methyl-3H-imidazo[4,5-c]pyridin-4-amine C7 H8 N4 VUSDRZRNZRBERR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.189 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.341	α = 90
b = 93.4	β = 112.85
c = 48.117	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-10-28 
Deposition Author(s): Mullins, E.A., Eichman, B.F.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	MCB-1122098

Revision History  

• Version 1.0: 2015-10-28
  Type: Initial release
  
• Version 1.1: 2015-11-18
  Changes: Database references
• Version 1.2: 2015-11-25
  Changes: Database references
• Version 1.3: 2017-09-13
  Changes: Author supporting evidence, Database references, Derived calculations
• Version 1.4: 2019-11-27
  Changes: Author supporting evidence
• Version 1.5: 2023-09-27
  Changes: Data collection, Database references, Refinement description