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PDBsum entry 1pu8

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protein ligands links
Hydrolase PDB id
1pu8
Jmol
Contents
Protein chains
216 a.a. *
Ligands
EA1 ×2
BME ×2
Waters ×161
* Residue conservation analysis
PDB id:
1pu8
Name: Hydrolase
Title: Crystal structure of h.Pylori 3-methyladenine DNA glycosylas bound to 1,n6-ethenoadenine
Structure: 3-methyladenine DNA glycosylase. Chain: a, b. Engineered: yes
Source: Helicobacter pylori. Organism_taxid: 210. Strain: 13-5. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.13Å     R-factor:   0.204     R-free:   0.230
Authors: B.F.Eichman,E.J.O'Rourke,J.P.Radicella,T.Ellenberger
Key ref: B.F.Eichman et al. (2003). Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases. EMBO J, 22, 4898-4909. PubMed id: 14517230
Date:
24-Jun-03     Release date:   07-Oct-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O25323  (O25323_HELPY) -  Endonuclease III
Seq:
Struc:
218 a.a.
216 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 9 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.4.2.99.18  - DNA-(apurinic or apyrimidinic site) lyase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
EMBO J 22:4898-4909 (2003)
PubMed id: 14517230  
 
 
Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases.
B.F.Eichman, E.J.O'Rourke, J.P.Radicella, T.Ellenberger.
 
  ABSTRACT  
 
DNA glycosylases catalyze the excision of chemically modified bases from DNA. Although most glycosylases are specific to a particular base, the 3-methyladenine (m3A) DNA glycosylases include both highly specific enzymes acting on a single modified base, and enzymes with broader specificity for alkylation-damaged DNA. Our structural understanding of these different enzymatic specificities is currently limited to crystal and NMR structures of the unliganded enzymes and complexes with abasic DNA inhibitors. Presented here are high-resolution crystal structures of the m3A DNA glycosylase from Helicobacter pylori (MagIII) in the unliganded form and bound to alkylated bases 3,9-dimethyladenine and 1,N6-ethenoadenine. These are the first structures of a nucleobase bound in the active site of a m3A glycosylase belonging to the helix-hairpin-helix superfamily. MagIII achieves its specificity for positively-charged m3A not by direct interactions with purine or methyl substituent atoms, but rather by stacking the base between two aromatic side chains in a pocket that excludes 7-methylguanine. We report base excision and DNA binding activities of MagIII active site mutants, together with a structural comparison of the HhH glycosylases.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21036872 M.I.Ponferrada-Marín, J.T.Parrilla-Doblas, T.Roldán-Arjona, and R.R.Ariza (2011).
A discontinuous DNA glycosylase domain in a family of enzymes that excise 5-methylcytosine.
  Nucleic Acids Res, 39, 1473-1484.  
20927102 E.H.Rubinson, A.S.Gowda, T.E.Spratt, B.Gold, and B.F.Eichman (2010).
An unprecedented nucleic acid capture mechanism for excision of DNA damage.
  Nature, 468, 406-411.
PDB codes: 3jx7 3jxy 3jxz 3jy1
19841264 S.Lee, and G.L.Verdine (2009).
Atomic substitution reveals the structural basis for substrate adenine recognition and removal by adenine DNA glycosylase.
  Proc Natl Acad Sci U S A, 106, 18497-18502.
PDB code: 3g0q
19200715 S.Schneider, S.Schorr, and T.Carell (2009).
Crystal structure analysis of DNA lesion repair and tolerance mechanisms.
  Curr Opin Struct Biol, 19, 87-95.  
18292897 I.Richter, J.Minari, P.Axe, J.P.Lowe, T.D.James, K.Sakurai, S.D.Bull, and J.S.Fossey (2008).
Intramolecular cation-pi interactions control the conformation of nonrestricted (phenylalkyl)pyridines.
  Chem Commun (Camb), (), 1082-1084.  
17410210 A.H.Metz, T.Hollis, and B.F.Eichman (2007).
DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
  EMBO J, 26, 2411-2420.
PDB codes: 2ofi 2ofk
17395642 B.Dalhus, I.H.Helle, P.H.Backe, I.Alseth, T.Rognes, M.Bjørås, and J.K.Laerdahl (2007).
Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats.
  Nucleic Acids Res, 35, 2451-2459.  
17396151 I.Leiros, M.P.Nabong, K.Grøsvik, J.Ringvoll, G.T.Haugland, L.Uldal, K.Reite, I.K.Olsbu, I.Knaevelsrud, E.Moe, O.A.Andersen, N.K.Birkeland, P.Ruoff, A.Klungland, and S.Bjelland (2007).
Structural basis for enzymatic excision of N1-methyladenine and N3-methylcytosine from DNA.
  EMBO J, 26, 2206-2217.
PDB codes: 2jhj 2jhn
16819516 D.T.Nair, R.E.Johnson, L.Prakash, S.Prakash, and A.K.Aggarwal (2006).
Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase iota.
  Nat Struct Mol Biol, 13, 619-625.
PDB codes: 2dpi 2dpj
15102448 J.C.Fromme, A.Banerjee, and G.L.Verdine (2004).
DNA glycosylase recognition and catalysis.
  Curr Opin Struct Biol, 14, 43-49.  
15128940 Y.Choi, J.J.Harada, R.B.Goldberg, and R.L.Fischer (2004).
An invariant aspartic acid in the DNA glycosylase domain of DEMETER is necessary for transcriptional activation of the imprinted MEDEA gene.
  Proc Natl Acad Sci U S A, 101, 7481-7486.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.