Two aspartate residues close to the lesion binding site of Agrobacterium (6‐4) photolyase are required for Mg²⁺ stimulation of DNA repair

Abstract

Prokaryotic (6‐4) photolyases branch at the base of the evolution of cryptochromes and photolyases. Prototypical members contain an iron–sulphur cluster which was lost in the evolution of the other groups. In the Agrobacterium (6‐4) photolyase PhrB, the repair of DNA lesions containing UV‐induced (6‐4) pyrimidine dimers is stimulated by Mg2+. We propose that Mg2+ is required for efficient lesion binding and for charge stabilization after electron transfer from the FADH− chromophore to the DNA lesion. Furthermore, two highly conserved Asp residues close to the DNA‐binding site are essential for the effect of Mg2+. Simulations show that two Mg2+ bind to the region around these residues. On the other hand, DNA repair by eukaryotic (6‐4) photolyases is not increased by Mg2+. In these photolyases, structurally overlapping regions contain no Asp but positively charged Lys or Arg. During the evolution of photolyases, the role of Mg2+ in charge stabilization and enhancement of DNA binding was therefore taken over by a postiviely charged amino acid. Besides PhrB, another prokaryotic (6‐4) photolyase from the marine cyanobacterium Prochlorococcus marinus, PromaPL, which contains no iron–sulphur cluster, was also investigated. This photolyase is stimulated by Mg2+ as well. The evolutionary loss of the iron–sulphur cluster due to limiting iron concentrations can occur in a marine environment as a result of iron deprivation. However, the evolutionary replacement of Mg2+ by a positively charged amino acid is unlikely to occur in a marine environment because the concentration of divalent cations in seawater is always sufficient. We therefore assume that this transition could have occurred in a freshwater environment.

DNA Photodamage and Repair: Computational Photobiology in Action

“…These calculations showed that the presence of a positively charged histidine decreases the energy of the reduced damage state by 7-20 kcal/mol, but the dead-end PCET is still possible. On the contrary, classical MD [122,133] shows that the double protonated histidine is more consistent with the experimental data concerning both structure and reactivity. Indeed, the RMSD of the histidine and the active site and the His-damage or His-FAD distances (among others) in Drosophilia melanogaster photolyase MD are more consistent with the crystallographic data in the presence of positively charged histidine.…”

“…The PhrB structure in interaction with DNA has not been resolved yet, but classical MD simulations starting form homologous models have been performed using the crystallographic structure of PhrB alone and the DNA damaged fragment from Drosophilia melanogaster photolyase repairing complex. These simulations reveal that two Mg 2+ enter in the active site and interact with two aspartates, which mutations to asparagine decrease the DNArepair activity, and with the damage in a similar way as the lysine and the arginine in Drosophilia melanogaster photolyase active site [122] (see figure XXXX). intermediate behavior [115].…”

Multiple Profile Models Extract Features from Protein Sequence Data and Resolve Functional Diversity of Very Different Protein Families

“…S3 and S4, Supplementary Material online; see also figs. 3 A , 3 C and 3 D ), is due to sequence divergence highlighting specific traits of the CRY Pro sequences such as the four FeS-binding cysteines which are missing in the (6-4) photolyase subgroup ( Ma et al 2019 ). In contrast, the CPD photolyase class divides in two distinguished subtrees corresponding to the subgroups Classes I and III CPD photolyase ( ) and Class II CPD photolyase ( ), which are not identified in the phylogenetic trees of the CPF family.…”

Identification and characterization of a prokaryotic 6-4 photolyase from Synechococcus elongatus with a deazariboflavin antenna chromophore

“…To explore the primary structural of prokaryotic 6–4 photolyases, six representatives including Af PhrB ( 17 , 18 ), Rs CryB ( 19 , 20 ), V. cholerae FeS-BCP ( Vc FeS-BCP) ( 21 ), Sphingomonas sp. FeS-BCP ( Sph PhrB) ( 22 ), P. marinus PromaPL ( 24 ), and Se PhrB were selected and aligned by using Clustal W ( 30 ). The result of the alignment was rendered by using ESPript 3.0 ( http://espript.ibcp.fr/ESPript/ESPript/ ) ( 31 ).…”

“…It was also shown that R. sphaeroides FeS-BCP ( Rs CryB) has bacterial cryptochrome functions that regulates photosynthesis and energy metabolism gene expression ( 23 ). Nevertheless, it was recently found that some other prokaryotic 6–4 photolyases containing no iron-sulfur cluster, such as Prochlorococcus marinus PromaPL, were classified into the same phylogenetic group together with FeS-BCPs ( 24 ). Therefore, it is better to name the entire group ‘prokaryotic 6–4 photolyases’, and to regard FeS-BCPs as a subtype of it.…”