A Prokaryotic (6‐4) Photolyase with a DMRL Chromophore and an Iron–Sulfur Cluster

Abstract

Photolyases are flavoproteins that repair UV ‐damaged DNA using the energy of sunlight. The flavin adenine dinucleotide ( FAD ) chromophores of photolyases and the related cryptochromes are bound to the chromophore pocket in a U‐shaped conformation. Often, a second cofactor serves as antenna chromophore in photolyases. This can be methenyltetrahydrofolate ( MTHF ), 8‐hydroxy‐7,8‐didemethyl‐5‐deazariboflavin (8‐ HDF ), FAD, or flavin mononucleotide ( FMN ). Two kinds of DNA lesions are produced by UV light, cyclobutan‐pyrimidine dimers ( CPDs ) or (6‐4) photoproducts. These lesions are repaired by two different types of photolyases, namely the CPDs and (6‐4) photolyases. Recently, a new phylogenetic group of the photolyase cryptochrome family termed iron–sulfur bacterial cryptochromes/photolyases (FeS‐BCP) was discovered. Two members of this group, CryB from Rhodobacter sphaeroides and ‘photolyase related protein’ (PhrB) from Agrobacterium tumefaciens , carry a new antenna chromophore, 6,7‐dimethyl 8‐ ribityl‐lumazin ( DMRL ), and incorporate an 4Fe‐4S cluster. PhrB acts as a (6‐4) photolyase with a repair activity that is higher for double‐stranded than for single‐stranded DNA . There are presently more than 900 prokaryotic PhrB homologs in the database in which the characteristic cysteine residues for incorporation of the Fe‐S cluster and other key amino acids are conserved. This new group of (6‐4) photolyases with an Fe‐S cluster is thus widely distributed among prokaryotes. Unlike in other photolyases, the loop connecting the N‐terminal and the C‐terminal domains of PhrB interacts with the DNA lesion. A C‐terminal extension, which could have a regulatory function, interacts with the DNA . The comparison between PhrB and eukaryotic (6‐4) photolyases highlights a conserved His residue which is located next to the DNA lesion. This residue serves probably as proton donor/acceptor during the repair cycle.

Divalent Cations Increase DNA Repair Activities of Bacterial (6‐4) Photolyases

“…We found that an improvement of DNA repair by Mg 2+ is restricted to members of the FeS‐BCP subfamily, although minor positive and negative Mg 2+ effects on photoreduction were found in different groups without clear correlations. Given the structural differences, the major evolutionary transition between FeS‐BCP proteins and other photolyases/cryptochromes may be associated with a loss of the Fe‐S cluster, replacement of the DMRL chromophore by other antenna chromophores and switch from the long interdomain linker between the antenna binding and catalytic domains to a region in the catalytic domain as DNA interacting loop . The present study shows that this kind of transition is also characterized by the loss of Mg 2+ dependency of the DNA repair function.…”

“…Phylogenetic tree of photolyases and cryptochromes. The tree is a simplified version of trees shown in previous publications in which only the groups of photolyase and cryptochromes are shown. Proteins used in the present study are indicated by bold letters.…”

Crystal Structures of Bacterial (6‐4) Photolyase Mutants with Impaired DNA Repair Activity

“…This mutant allowed us to investigate the specific role of DMRL in the wild‐type PhrB. As described before, the PhrB Y424F mutant exhibits loss of both DNA‐binding and DNA repair activity .…”

Key Amino Acids in the Bacterial (6-4) Photolyase PhrB from Agrobacterium fabrum

“…Photolyases are flavoproteins that repair UV-damaged DNA in a light-dependent fashion, cryptochromes are related proteins without repair activity that serve as photoreceptors or compounds of the inner clock. The family of photolyases and cryptochromes may be divided into seven major phylogenetic groups: CPD photolyases class I, II and III, Cry-DASH proteins, eukaryotic (6–4) photolyases and animal cryptochromes, plant cryptochromes and prokaryotic FeS-BCP (Fe-S bacterial cryptochromes and photolyases) proteins [ 1 , 2 ]. The terms CPD- and (6–4) photolyases refer to the kind of lesions that are repaired by these proteins, which are cyclo pyrimidine dimers and (6–4) photoproducts, respectively [ 3 ].…”