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PDBsum entry 2ofk

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
2ofk
Jmol
Contents
Protein chains
182 a.a. *
Ligands
PGE ×8
Metals
_ZN ×2
Waters ×328
* Residue conservation analysis
PDB id:
2ofk
Name: Hydrolase
Title: Crystal structure of 3-methyladenine DNA glycosylase i (tag)
Structure: 3-methyladenine DNA glycosylase i, constitutive. Chain: a, b. Synonym: 3-methyladenine DNA glycosylase i. Engineered: yes
Source: Salmonella typhi. Organism_taxid: 601. Gene: tag. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.50Å     R-factor:   0.163     R-free:   0.196
Authors: A.H.Metz,T.Hollis,B.F.Eichman
Key ref:
A.H.Metz et al. (2007). DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG). EMBO J, 26, 2411-2420. PubMed id: 17410210 DOI: 10.1038/sj.emboj.7601649
Date:
03-Jan-07     Release date:   15-May-07    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q8Z2A5  (Q8Z2A5_SALTI) -  3-methyladenine DNA glycosylase I
Seq:
Struc:
193 a.a.
182 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   2 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
DOI no: 10.1038/sj.emboj.7601649 EMBO J 26:2411-2420 (2007)
PubMed id: 17410210  
 
 
DNA damage recognition and repair by 3-methyladenine DNA glycosylase I (TAG).
A.H.Metz, T.Hollis, B.F.Eichman.
 
  ABSTRACT  
 
DNA glycosylases help maintain the genome by excising chemically modified bases from DNA. Escherichia coli 3-methyladenine DNA glycosylase I (TAG) specifically catalyzes the removal of the cytotoxic lesion 3-methyladenine (3mA). The molecular basis for the enzymatic recognition and removal of 3mA from DNA is currently a matter of speculation, in part owing to the lack of a structure of a 3mA-specific glycosylase bound to damaged DNA. Here, high-resolution crystal structures of Salmonella typhi TAG in the unliganded form and in a ternary product complex with abasic DNA and 3mA nucleobase are presented. Despite its structural similarity to the helix-hairpin-helix superfamily of DNA glycosylases, TAG has evolved a modified strategy for engaging damaged DNA. In contrast to other glycosylase-DNA structures, the abasic ribose is not flipped into the TAG active site. This is the first structural demonstration that conformational relaxation must occur in the DNA upon base hydrolysis. Together with mutational studies of TAG enzymatic activity, these data provide a model for the specific recognition and hydrolysis of 3mA from DNA.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 The structure of the TAG–DNA complex. (A) The crystallographic model of TAG (blue ribbons; yellow HhH motif) bound to DNA (orange sticks) and 3mA (ball-and-stick). The abasic site in the DNA is highlighted in green and the coordinated Zn^2+ ion is shown as a magenta sphere. (B) Schematic representation showing the electrostatic (dashed lines) and van der Waals (wavy lines) interactions between protein side-chain and main-chain (mc) atoms with the DNA.
Figure 3.
Figure 3 TAG interrogation of the DNA base stack. TAG binds the DNA damage site by intercalating side chains (blue) into both the lesioned (yellow) and non-lesioned (gold) DNA strands. Hydrogen bonds to the estranged thymine are shown as dashed lines and the 3mA base is colored green.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2007, 26, 2411-2420) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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
19880517 A.Maiti, M.T.Morgan, and A.C.Drohat (2009).
Role of two strictly conserved residues in nucleotide flipping and N-glycosylic bond cleavage by human thymine DNA glycosylase.
  J Biol Chem, 284, 36680-36688.  
18065420 P.D.Robertson, E.M.Warren, H.Zhang, D.B.Friedman, J.W.Lary, J.L.Cole, A.V.Tutter, J.C.Walter, E.Fanning, and B.F.Eichman (2008).
Domain architecture and biochemical characterization of vertebrate mcm10.
  J Biol Chem, 283, 3338-3348.  
18083815 R.P.da Rocha, A.C.Paquola, M.d.o. .V.Marques, C.F.Menck, and R.S.Galhardo (2008).
Characterization of the SOS regulon of Caulobacter crescentus.
  J Bacteriol, 190, 1209-1218.  
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.