2JHN | pdb_00002jhn

3-methyladenine dna-glycosylase from Archaeoglobus fulgidus

• PDB DOI: https://doi.org/10.2210/pdb2JHN/pdb

• Classification: HYDROLASE
• Organism(s): Archaeoglobus fulgidus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-02-22 Released: 2007-04-10 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

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

• PubMed: 17396151 
• DOI: https://doi.org/10.1038/sj.emboj.7601662
• Primary Citation Related Structures: 
  2JHJ, 2JHN


• 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 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.

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Organizational Affiliation: 
• The Norwegian Structural Biology Centre, University of Tromsø, Tromsø, Norway.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 70.85 kDa 
• Atom Count: 5,493 
• Modeled Residue Count: 584 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-METHYLADENINE DNA-GLYCOSYLASE	A, B	295	Archaeoglobus fulgidus	Mutation(s): 1  EC: 3.2.2.21
UniProt
Find proteins for O28163 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O28163  Go to UniProtKB:  O28163

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MBO	C [auth A], J [auth B]	MERCURIBENZOIC ACID C7 H5 Hg O2 FVFZSVRSDNUCGG-UHFFFAOYSA-N
HG	D [auth A], K [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
MES	H [auth A], O [auth B], P [auth B], Q [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
GOL	G [auth A], I [auth A], N [auth B], R [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	E [auth A], F [auth A], L [auth B], M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.223 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.494	α = 90
b = 49.968	β = 107.43
c = 105.798	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
SHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-04-10 
Deposition Author(s): 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.

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
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other