PDBsum entry 3cwt

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protein dna_rna Protein-protein interface(s) links
Hydrolase/DNA PDB id
Protein chains
282 a.a. *
Waters ×124
* Residue conservation analysis
PDB id:
Name: Hydrolase/DNA
Title: Crystal structure of an alka host/guest complex 2'-fluoro- 2'-deoxyinosine:adenine base pair
Structure: DNA-3-methyladenine glycosylase 2. Chain: a, b, c, d. Synonym: DNA-3-methyladenine glycosylase ii, 3- methyladenine-DNA glycosylase ii, inducible, tag ii, DNA-3- methyladenine glycosidase ii. Engineered: yes. DNA (5'-d( Dgp Dap Dcp Dap Dtp Dgp Dap (2Fi) p Dtp Dgp Dcp Dc)-3'). Chain: e, g.
Source: Escherichia coli. Gene: alka, aida. Expressed in: escherichia coli. Synthetic: yes. Synthetic: yes
2.30Å     R-factor:   0.239     R-free:   0.280
Authors: B.R.Bowman,S.Lee,S.Wang,G.L.Verdine
Key ref:
B.R.Bowman et al. (2008). Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA. Structure, 16, 1166-1174. PubMed id: 18682218 DOI: 10.1016/j.str.2008.04.012
22-Apr-08     Release date:   02-Sep-08    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P04395  (3MG2_ECOLI) -  DNA-3-methyladenine glycosylase 2
282 a.a.
282 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - DNA-3-methyladenine glycosylase Ii.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine, and 7-methyladenine.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to DNA damage stimulus   4 terms 
  Biochemical function     catalytic activity     7 terms  


DOI no: 10.1016/j.str.2008.04.012 Structure 16:1166-1174 (2008)
PubMed id: 18682218  
Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA.
B.R.Bowman, S.Lee, S.Wang, G.L.Verdine.
The constant attack on DNA by endogenous and exogenous agents gives rise to nucleobase modifications that cause mutations, which can lead to cancer. Visualizing the effects of these lesions on the structure of duplex DNA is key to understanding their biologic consequences. The most definitive method of obtaining such structures, X-ray crystallography, is troublesome to employ owing to the difficulty of obtaining diffraction-quality crystals of DNA. Here, we present a crystallization system that uses a protein, the DNA glycosylase AlkA, as a scaffold to mediate the crystallization of lesion-containing duplex DNA. We demonstrate the use of this system to facilitate the rapid structure determination of DNA containing the lesion 8-oxoguanine in several different sequence contexts, and also deoxyinosine and 1,N(6)-ethenoadenine, each stabilized as the corresponding 2'-flouro analog. The structures of 8-oxoguanine provide a correct atomic-level view of this important endogenous lesion in DNA.
  Selected figure(s)  
Figure 2.
Figure 2. Cα Superposition of the AlkA Azaribose LRC Structure onto an AlkA/DNA Subunit from the AlkA HGC
The rmsd of the LRC (the protein is colored cyan as in Figure 1B; DNA colored white) onto the HGC subunit (colored as in Figure 1C) is 0.37 Å. The crimson dot denotes the position of the phosphate that hydrogen bonds with the protein backbone at positions 249 and 251 (yellow loop); this phosphate is the only element of the otherwise naked central portion of the DNA that is contacted by the protein. The major sites of protein:DNA interaction are colored as in Figure 1C.
Figure 5.
Figure 5. B-Form DNA Containing oxoG:dA or oxoG:dC Base Pairs
(A–C) The oxoG:C base pairs (left column) with oxoG in the (A) one position, (B) six position, and (C) eight position within the DNA duplex. In the right column, G:C structures in the same positions within the DNA as the respective lesion are shown.
(D) Structure of oxoG base paired with adenine. The color scheme, F[o] − F[c] electron density map and hydrogen bonding are represented as in Figure 3.
  The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1166-1174) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22659876 C.Yi, B.Chen, B.Qi, W.Zhang, G.Jia, L.Zhang, C.J.Li, A.R.Dinner, C.G.Yang, and C.He (2012).
Duplex interrogation by a direct DNA repair protein in search of base damage.
  Nat Struct Mol Biol, 19, 671-676.
PDB codes: 3rzg 3rzh 3rzj 3rzk 3rzl 3rzm 3s57 3s5a
21474392 A.Maiti, and A.C.Drohat (2011).
Dependence of substrate binding and catalysis on pH, ionic strength, and temperature for thymine DNA glycosylase: Insights into recognition and processing of G·T mispairs.
  DNA Repair (Amst), 10, 545-553.  
19889642 Y.Qi, M.C.Spong, K.Nam, M.Karplus, and G.L.Verdine (2010).
Entrapment and structure of an extrahelical guanine attempting to enter the active site of a bacterial DNA glycosylase, MutM.
  J Biol Chem, 285, 1468-1478.
PDB codes: 3jr4 3jr5
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
20010681 Y.Qi, M.C.Spong, K.Nam, A.Banerjee, S.Jiralerspong, M.Karplus, and G.L.Verdine (2009).
Encounter and extrusion of an intrahelical lesion by a DNA repair enzyme.
  Nature, 462, 762-766.
PDB codes: 3go8 3gp1 3gpp 3gpu 3gpx 3gpy 3gq3 3gq4 3gq5
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