Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor.
UV exposure of DNA molecules induces serious DNA lesions. The cyclobutane pyrimidine dimer (CPD) photolyase repairs CPD-type - lesions by using the energy of visible light. Two chromophores for different roles have been found in this enzyme family; one catalyzes the CPD repair reaction and the other works as an antenna pigment that harvests photon energy. The catalytic cofactor of all known photolyases is FAD, whereas several light-harvesting cofactors are found. Currently, 5,10-methenyltetrahydrofolate (MTHF), 8-hydroxy-5-deaza-riboflavin (8-HDF) and FMN are the known light-harvesting cofactors, and some photolyases lack the chromophore. Three crystal structures of photolyases from Escherichia coli (Ec-photolyase), Anacystis nidulans (An-photolyase), and Thermus thermophilus (Tt-photolyase) have been determined; however, no archaeal photolyase structure is available. A similarity search of archaeal genomic data indicated the presence of a homologous gene, ST0889, on Sulfolobus tokodaii strain7. An enzymatic assay reveals that ST0889 encodes photolyase from S. tokodaii (St-photolyase). We have determined the crystal structure of the St-photolyase protein to confirm its structural features and to investigate the mechanism of the archaeal DNA repair system with light energy. The crystal structure of the St-photolyase is superimposed very well on the three known photolyases including the catalytic cofactor FAD. Surprisingly, another FAD molecule is found at the position of the light-harvesting cofactor. This second FAD molecule is well accommodated in the crystal structure, suggesting that FAD works as a novel light-harvesting cofactor of photolyase. In addition, two of the four CPD recognition residues in the crystal structure of An-photolyase are not found in St-photolyase, which might utilize a different mechanism to recognize the CPD from that of An-photolyase.
Fujihashi
Masahiro
M
Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
Numoto
Nobutaka
N
Kobayashi
Yukiko
Y
Mizushima
Akira
A
Tsujimura
Masanari
M
Nakamura
Akira
A
Kawarabayasi
Yutaka
Y
Miki
Kunio
K
D000595:Amino Acid Sequence; D002384:Catalysis; D018360:Crystallography, X-Ray; D000458:Cyanobacteria / Q000201:enzymology; D004247:DNA / Q000737:chemistry; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000737:chemistry*; D004926:Escherichia coli / Q000201:enzymology; D005182:Flavin-Adenine Dinucleotide / Q000737:chemistry*; D020745:Genome, Archaeal; D045342:Light-Harvesting Protein Complexes / Q000737:chemistry*; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D017433:Protein Structure, Secondary; D016944:Sulfolobus / Q000201:enzymology*; D016963:Thermus thermophilus / Q000201:enzymology
D045342:Light-Harvesting Protein Complexes; D005182:Flavin-Adenine Dinucleotide; D004247:DNA; D004255:Deoxyribodipyrimidine Photo-Lyase