PDBsum entry 1k82

Hydrolase/DNA

PDB id: 1k82

Contents

Protein chains

260 a.a. *

DNA/RNA

Metals

_ZN ×4

Waters ×499

* Residue conservation analysis

PDB id:

1k82

Name:

Hydrolase/DNA

Title:

Crystal structure of e.Coli formamidopyrimidine-DNA glycosylase (fpg) covalently trapped with DNA

Structure:

5'-d( Gp Gp Cp Tp Tp Cp Cp Tp Cp Cp Tp Gp G)-3'. Chain: e, f, g, h. Synonym: fapy-DNA glycosylase, fpg. Engineered: yes. 5'-d( Cp Cp Ap Gp Gp Ap (Ped)p Gp Ap Ap Gp Cp C)-3'. Chain: i, j, k, l. Engineered: yes. Formamidopyrimidine-DNA glycosylase. Chain: a, b, c, d.

Source:

Synthetic: yes. Escherichia coli. Organism_taxid: 562. Gene: fpg. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dodecamer (from PQS)

Resolution:

2.10Å R-factor: 0.214 R-free: 0.265

Authors:

R.Gilboa,D.O.Zharkov,G.Golan,A.S.Fernandes,S.E.Gerchman,E.Matz, J.H.Kycia,A.P.Grollman,G.Shoham

Key ref:

R.Gilboa et al. (2002). Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. J Biol Chem, 277, 19811-19816. PubMed id: 11912217 DOI: 10.1074/jbc.M202058200

Date:

22-Oct-01 Release date: 14-Jun-02

Protein chains

P05523  (FPG_ECOLI) -  Formamidopyrimidine-DNA glycosylase from Escherichia coli (strain K12)

Seq: 269 a.a.

Struc: 260 a.a.

DNA/RNA chains

G-G-C-T-T-C-C-T-C-C-T-G-G 13 bases

C-C-A-G-G-A-PED-G-A-A-G-C-C 13 bases

G-G-C-T-T-C-C-T-C-C-T-G-G 13 bases

C-C-A-G-G-A-PED-G-A-A-G-C-C 13 bases

G-G-C-T-T-C-C-T-C-C-T-G-G 13 bases

C-C-A-G-G-A-PED-G-A-A-G-C-C 13 bases

G-G-C-T-T-C-C-T-C-C-T-G-G 13 bases

C-C-A-G-G-A-PED-G-A-A-G-C-C 13 bases

Enzyme reactions

• Enzyme class 2: E.C.3.2.2.23 - DNA-formamidopyrimidine glycosylase.
• Reaction: Hydrolysis of DNA containing ring-opened N(7)-methylguanine residues, releasing 2,6-diamino-4-hydroxy-5-(N-methyl)formamidopyrimide.
• Enzyme class 3: E.C.4.2.99.18 - DNA-(apurinic or apyrimidinic site) lyase.
• Reaction: 2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)- 2'-deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho- 2'-deoxyribonucleoside-DNA + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1074/jbc.M202058200

J Biol Chem 277:19811-19816 (2002)

PubMed id: 11912217

Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.

R.Gilboa, D.O.Zharkov, G.Golan, A.S.Fernandes, S.E.Gerchman, E.Matz, J.H.Kycia, A.P.Grollman, G.Shoham.

ABSTRACT

Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. The Schiff base intermediate formed during this reaction between Escherichia coli Fpg and DNA was trapped by reduction with sodium borohydride, and the structure of the resulting covalently cross-linked complex was determined at a 2.1-A resolution. Fpg is a bilobal protein with a wide, positively charged DNA-binding groove. It possesses a conserved zinc finger and a helix-two turn-helix motif that participate in DNA binding. The absolutely conserved residues Lys-56, His-70, Asn-168, and Arg-258 form hydrogen bonds to the phosphodiester backbone of DNA, which is sharply kinked at the lesion site. Residues Met-73, Arg-109, and Phe-110 are inserted into the DNA helix, filling the void created by nucleotide eversion. A deep hydrophobic pocket in the active site is positioned to accommodate an everted base. Structural analysis of the Fpg-DNA complex reveals essential features of damage recognition and the catalytic mechanism of Fpg.

Selected figure(s)

Figure 4.
Fig. 4. Schematic representation of Fpg-DNA interactions. The central nucleotides of the modified and complementary strands are 8-oxoG0 and C^(0), respectively. Nucleotides are numbered as shown with those in the complementary strand in parentheses.

Figure 6.
Fig. 6. Scheme of principal steps in the sequence of reactions catalyzed by Fpg, showing catalytically important amino acid residues. Nucleophilic attack at C1' and protonation at O4' (a) lead to base displacement and deoxyribose ring opening. A Schiff base involving Pro-1 is formed with O4' stabilized by hydrogen bonding to Glu-2. b, following abstraction of the 2' proton of deoxyribose by a general base, Lys-56 protonates the 3'-phosphate leading to -elimination (c). Deprotonation of C4', now vinilogous to C1', is followed by protonation of the 5'-phosphate by Arg-258 and the second -elimination event (c).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 19811-19816) copyright 2002.

Figures were selected by an automated process.