PDBsum entry: 1diz

Hydrolase/DNA

PDB id: 1diz

Contents

Protein chains

282 a.a. *

DNA/RNA

Metals

_NA ×2

Waters ×207

* Residue conservation analysis

PDB id:

1diz

Name:

Hydrolase/DNA

Title:

Crystal structure of e. Coli 3-methyladenine DNA glycosylase (alka) complexed with DNA

Structure:

DNA (5'-d( Gp Ap Cp Ap Tp Gp Ap (Nri) p Tp Gp Cp Cp T)-3'). Chain: c, e. Engineered: yes. DNA (5'- d( Gp Gp Cp Ap Ap Tp Cp Ap Tp Gp Tp Cp A)-3'). Chain: d, f. Engineered: yes. 3-methyladenine DNA glycosylase ii.

Source:

Synthetic: yes. Other_details: this sequence occurs naturally in e. Coli. Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562

Biol. unit:

Hexamer (from PQS)

Resolution:

2.50Å R-factor: 0.250 R-free: 0.290

Authors:

T.Hollis,Y.Ichikawa,T.E.Ellenberger

Key ref:

T.Hollis et al. (2000). DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA. EMBO J, 19, 758-766. PubMed id: 10675345 DOI: 10.1093/emboj/19.4.758

Date:

30-Nov-99 Release date: 20-Mar-00

Protein chains

P04395  (3MG2_ECOLI) -  DNA-3-methyladenine glycosylase 2

Seq: 282 a.a.

Struc: 282 a.a.

Enzyme reactions

• Enzyme class: E.C.3.2.2.21 - DNA-3-methyladenine glycosylase Ii.
• Reaction: Hydrolysis of alkylated DNA, releasing 3-methyladenine, 3-methylguanine, 7-methylguanine, and 7-methyladenine.

 Gene Ontology (GO) functional annotation 

• Cellular component: cytoplasm (1 term)
• Biological process: response to DNA damage stimulus (4 terms)
• Biochemical function: catalytic activity (8 terms)

DOI no: 10.1093/emboj/19.4.758

EMBO J 19:758-766 (2000)

PubMed id: 10675345

DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA.

T.Hollis, Y.Ichikawa, T.Ellenberger.

ABSTRACT

The Escherichia coli AlkA protein is a base excision repair glycosylase that removes a variety of alkylated bases from DNA. The 2.5 A crystal structure of AlkA complexed to DNA shows a large distortion in the bound DNA. The enzyme flips a 1-azaribose abasic nucleotide out of DNA and induces a 66 degrees bend in the DNA with a marked widening of the minor groove. The position of the 1-azaribose in the enzyme active site suggests an S(N)1-type mechanism for the glycosylase reaction, in which the essential catalytic Asp238 provides direct assistance for base removal. Catalytic selectivity might result from the enhanced stacking of positively charged, alkylated bases against the aromatic side chain of Trp272 in conjunction with the relative ease of cleaving the weakened glycosylic bond of these modified nucleotides. The structure of the AlkA-DNA complex offers the first glimpse of a helix-hairpin-helix (HhH) glycosylase complexed to DNA. Modeling studies suggest that other HhH glycosylases can bind to DNA in a similar manner.

Selected figure(s)

Figure 5.
Figure 5 A 3-methyladenine substrate modeled in AlkA's active site. 3-methyladenine (pink) was superimposed on the 1-azaribose moiety in the crystal structure of the AlkA–DNA complex. In the resulting model, the 3-methyladenine base stacks face-to-face against Trp272 and makes edge-on contacts with Tyr222. The open architecture of AlkA's substrate-binding pocket would accommodate many types of modified bases. Trp218 is located behind the ribose of the flipped out nucleotide, leaving no room for a water nucleophile (cf. Figure 6).

Figure 6.
Figure 6 Mechanistic implications of the AlkA active site. The closely interacting van der Waals surfaces of the protein (green) and the DNA (yellow) leave no room between the deoxyribose of a flipped out nucleotide and Trp218 to position a water molecule (red) for an attack on the back of the glycosylic bond. This is strong evidence against a direct displacement (S[N]2) mechanism of glycosylic bond cleavage (see text for details).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 758-766) copyright 2000.

Figures were selected by the author.