2JHN

3-methyladenine dna-glycosylase from Archaeoglobus fulgidus

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Structural Basis for Enzymatic Excision of N1-Methyladenine and N3-Methylcytosine from DNA

Leiros, I., Nabong, M.P., Grosvik, K., Ringvoll, J., Haugland, G.T., Uldal, L., Reite, K., Olsbu, I.K., Knaevelsrud, I., Moe, E., Andersen, O.A., Birkeland, N.K., Ruoff, P., Klungland, A., Bjelland, S.

(2007) EMBO J 26: 2206

  • DOI: 10.1038/sj.emboj.7601662
  • Primary Citation of Related Structures:  
    2JHN, 2JHJ

  • PubMed Abstract: 

    • N(1)-methyladenine (m(1)A) and N(3)-methylcytosine (m(3)C) are major toxic and mutagenic lesions induced by alkylation in single-stranded DNA. In bacteria and mammals, m(1)A and m(3)C were recently shown to be repaired by AlkB-mediated oxidative deme ...

    N(1)-methyladenine (m(1)A) and N(3)-methylcytosine (m(3)C) are major toxic and mutagenic lesions induced by alkylation in single-stranded DNA. In bacteria and mammals, m(1)A and m(3)C were recently shown to be repaired by AlkB-mediated oxidative demethylation, a direct DNA damage reversal mechanism. No AlkB gene homologues have been identified in Archaea. We report that m(1)A and m(3)C are repaired by the AfAlkA base excision repair glycosylase of Archaeoglobus fulgidus, suggesting a different repair mechanism for these lesions in the third domain of life. In addition, AfAlkA was found to effect a robust excision of 1,N(6)-ethenoadenine. We present a high-resolution crystal structure of AfAlkA, which, together with the characterization of several site-directed mutants, forms a molecular rationalization for the newly discovered base excision activity.

    Organizational Affiliation: 

    The Norwegian Structural Biology Centre, University of Tromsø, Tromsø, Norway.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-METHYLADENINE DNA-GLYCOSYLASEA, B295Archaeoglobus fulgidusMutation(s): 1 
EC: 3.2.2.21
Find proteins for O28163 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O28163 
Go to UniProtKB:  O28163
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MBO
Query on MBO
Download CCD File 
A, B
MERCURIBENZOIC ACID
C7 H5 Hg O2
FVFZSVRSDNUCGG-UHFFFAOYSA-N		 Ligand Interaction
HG
Query on HG
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A, B
MERCURY (II) ION
Hg
BQPIGGFYSBELGY-UHFFFAOYSA-N		 Ligand Interaction
MES
Query on MES
Download CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N		 Ligand Interaction
GOL
Query on GOL
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A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.494α = 90
b = 49.968β = 107.43
c = 105.798γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance