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1k82

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This article has been automatically seeded. Changes to this page should pertain to the PDB entry only and not to the protein or biomolecule in general.

1k82, resolution 2.10Å ()

Ligands:

Non-Standard Residues:

Gene:

fpg (Escherichia coli)

Activity:

DNA-formamidopyrimidine glycosylase, with EC number 3.2.2.23

Domains:

H2TH, Fapy_DNA_glyco, PRK01103

Structural annotation:
Resources:	InterPro : Ipr010979, Ipr012319, Ipr015887, Ipr015886, Ipr000214, Ipr010663 Pfam : PF01149, PF06827, PF06831 SCOP : d1k82a1, d1k82a2, d1k82a3, d1k82b1, d1k82b2, d1k82b3, d1k82c3, d1k82c2, d1k82c1, d1k82d3, d1k82d2, d1k82d1 UniProt : P05523

Functional annotation:
Biological process:	base-excision repair response to DNA damage stimulus metabolic process DNA repair
Molecular function:	metal ion binding hydrolase activity, acting on glycosyl bonds DNA-(apurinic or apyrimidinic site) lyase activity zinc ion binding lyase activity hydrolase activity DNA binding damaged DNA binding oxidized purine base lesion DNA N-glycosylase activity catalytic activity

Evolutionary conservation:

Toggle Conservation Colors:

Rows = identical sequences:

Further Information:

Caveats,

Explanation,
Complete Results at ConSurfDB

Resources:

FirstGlance, OCA, PDBsum, RCSB

Coordinates:

save as pdb, mmCIF, xml

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

Publication Abstract from PubMed

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.

Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA., Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G, J Biol Chem. 2002 May 31;277(22):19811-6. Epub 2002 Mar 23. PMID:11912217

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1K82 is a 12 chains structure of sequences from Escherichia coli. Full crystallographic information is available from OCA.

Reference

Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G. Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. J Biol Chem. 2002 May 31;277(22):19811-6. Epub 2002 Mar 23. PMID:11912217 doi:10.1074/jbc.M202058200

Page seeded by OCA on Wed Feb 18 03:48:03 2009

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1k82

From Proteopedia

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

About this Structure

Reference

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