1DNP

STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE

Summary for 1DNP

• Entry DOI: 10.2210/pdb1dnp/pdb
• Descriptor: DNA PHOTOLYASE, FLAVIN-ADENINE DINUCLEOTIDE, 5,10-METHENYL-6,7,8-TRIHYDROFOLIC ACID, ... (4 entities in total)
• Functional Keywords: dna repair, electron transfer, excitation energy transfer, lyase, carbon-carbon, lyase (carbon-carbon)
• Biological source: Escherichia coli
• Total number of polymer chains: 2
• Total formula weight: 109689.10

Authors

Park, H.-W.,Sancar, A.,Deisenhofer, J. (deposition date: 1995-07-03, release date: 1996-08-01, Last modification date: 2024-02-07)

Primary citation

Park, H.W.,Kim, S.T.,Sancar, A.,Deisenhofer, J.
Crystal structure of DNA photolyase from Escherichia coli.
Science, 268:1866-1872, 1995

PubMed Abstract: Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr <> Pyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 A resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal alpha/beta domain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 A. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a Pyr <> Pyr dinucleotide, suggesting that the Pyr <> Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr <> Pyr occurs over van der Waals contact distance.

PubMed: 7604260

Experimental method

X-RAY DIFFRACTION (2.3 Å)