3OH6 | pdb_00003oh6

AlkA Undamaged DNA Complex: Interrogation of a C:G base pair

• PDB DOI: https://doi.org/10.2210/pdb3OH6/pdb
• NAKB: 3OH6

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-08-17 Released: 2010-09-15 
• Deposition Author(s): Bowman, B.R., Lee, S., Wang, S., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.227 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Structure of Escherichia coli AlkA in Complex with Undamaged DNA.

Bowman, B.R., Lee, S., Wang, S., Verdine, G.L.

(2010) J Biological Chem 285: 35783-35791

• PubMed: 20843803 
• DOI: https://doi.org/10.1074/jbc.M110.155663
• Primary Citation Related Structures: 
  3OGD, 3OH6, 3OH9


• PubMed Abstract: 
  

  Because DNA damage is so rare, DNA glycosylases interact for the most part with undamaged DNA. Whereas the structural basis for recognition of DNA lesions by glycosylases has been studied extensively, less is known about the nature of the interaction between these proteins and undamaged DNA. Here we report the crystal structures of the DNA glycosylase AlkA in complex with undamaged DNA. The structures revealed a recognition mode in which the DNA is nearly straight, with no amino acid side chains inserted into the duplex, and the target base pair is fully intrahelical. A comparison of the present structures with that of AlkA recognizing an extrahelical lesion revealed conformational changes in both the DNA and protein as the glycosylase transitions from the interrogation of undamaged DNA to catalysis of nucleobase excision. Modeling studies with the cytotoxic lesion 3-methyladenine and accompanying biochemical experiments suggested that AlkA actively interrogates the minor groove of the DNA while probing for the presence of lesions.

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Organizational Affiliation: 
• Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.21 kDa 
• Atom Count: 2,718 
• Modeled Residue Count: 311 
• Deposited Residue Count: 312 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-3-methyladenine glycosylase 2	A	289	Escherichia coli K-12	Mutation(s): 1  Gene Names: aidA, alkA, b2068, JW2053 EC: 3.2.2.21
UniProt
Find proteins for P04395 (Escherichia coli (strain K12)) Explore P04395  Go to UniProtKB:  P04395

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*AP*TP*TP*CP*AP*TP*GP*TP*C)-3'	B	11	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*GP*AP*CP*AP*(BRU)P*GP*AP*AP*(BRU)P*GP*CP*C)-3'	C	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.227 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.3	α = 90
b = 140.3	β = 90
c = 94.8	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Bowman, B.R., Lee, S., Wang, S., Verdine, G.L.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description