Structure of an unusual 3-Methyladenine DNA Glycosylase II (Alka) from Deinococcus radiodurans

Experimental Data Snapshot

  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

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Structure-function studies of an unusual 3-methyladenine DNA glycosylase II (AlkA) from Deinococcus radiodurans.

Moe, E.Hall, D.R.Leiros, I.Monsen, V.T.Timmins, J.McSweeney, S.

(2012) Acta Crystallogr D Biol Crystallogr 68: 703-712

  • DOI: https://doi.org/10.1107/S090744491200947X
  • Primary Citation of Related Structures:  
    2YG8, 2YG9

  • PubMed Abstract: 

    3-Methyladenine DNA glycosylase II (AlkA) is a DNA-repair enzyme that removes alkylated bases in DNA via the base-excision repair (BER) pathway. The enzyme belongs to the helix-hairpin-helix (HhH) superfamily of DNA glycosylases and possesses broad substrate specificity. In the genome of Deinococcus radiodurans, two genes encoding putative AlkA have been identified (Dr_2074 and Dr_2584). Dr_2074 is a homologue of human AlkA (MPG or AAG) and Dr_2584 is a homologue of bacterial AlkAs. Here, the three-dimensional structure of Dr_2584 (DrAlkA2) is presented and compared with the previously determined structure of Escherichia coli AlkA (EcAlkA). The results show that the enzyme consists of two helical-bundle domains separated by a wide DNA-binding cleft and contains an HhH motif. Overall, the protein fold is similar to the two helical-bundle domains of EcAlkA, while the third N-terminal mixed α/β domain observed in EcAlkA is absent. Substrate-specificity analyses show that DrAlkA2, like EcAlkA, is able to remove both 3-methyladenine (3meA) and 7-methylguanine (7meG) from DNA; however, the enzyme possesses no activity towards 1,N(6)-ethenoadenine (ℇA) and hypoxanthine (Hx). In addition, it shows activity towards the AlkB dioxygenase substrates 3-methylcytosine (3meC) and 1-methyladenine (1meA). Thus, the enzyme seems to preferentially repair methylated bases with weakened N-glycosidic bonds; this is an unusual specificity for a bacterial AlkA protein and is probably dictated by a combination of the wide DNA-binding cleft and a highly accessible specificity pocket.

  • Organizational Affiliation

    The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-3-methyladenine glycosidase II, putative
A, B
225Deinococcus radioduransMutation(s): 0 
Gene Names: DR_2584
Find proteins for Q9RRB0 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1))
Explore Q9RRB0 
Go to UniProtKB:  Q9RRB0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9RRB0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.95 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.311α = 90
b = 51.372β = 99.71
c = 90.039γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references, Non-polymer description, Version format compliance
  • Version 1.2: 2012-06-20
    Changes: Other
  • Version 1.3: 2018-12-05
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description