1K82

Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA

Summary for 1K82

• Entry DOI: 10.2210/pdb1k82/pdb
• Descriptor: 5'-D(*GP*GP*CP*TP*TP*CP*CP*TP*CP*CP*TP*GP*G)-3', 5'-D(*CP*CP*AP*GP*GP*AP*(PED)P*GP*AP*AP*GP*CP*C)-3', formamidopyrimidine-DNA glycosylase, ... (5 entities in total)
• Functional Keywords: protein-dna complex, dna repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase-dna complex, hydrolase/dna
• Biological source: Escherichia coli
• Total number of polymer chains: 12
• Total formula weight: 152269.58

Authors

Gilboa, R.,Zharkov, D.O.,Golan, G.,Fernandes, A.S.,Gerchman, S.E.,Matz, E.,Kycia, J.H.,Grollman, A.P.,Shoham, G. (deposition date: 2001-10-22, release date: 2002-06-14, Last modification date: 2023-08-16)

Primary citation

Gilboa, R.,Zharkov, D.O.,Golan, G.,Fernandes, A.S.,Gerchman, S.E.,Matz, E.,Kycia, J.H.,Grollman, A.P.,Shoham, G.
Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.
J.Biol.Chem., 277:19811-19816, 2002

PubMed 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.

PubMed: 11912217
DOI: 10.1074/jbc.M202058200

Experimental method

X-RAY DIFFRACTION (2.1 Å)