Structure of the bifunctional cryptochrome aCRY from Chlamydomonas reinhardtii

Abstract

Photolyases and cryptochromes form an almost ubiquitous family of blue light photoreceptors involved in the repair and maintenance of DNA integrity or regulatory control. We found that one cryptochrome from the green alga Chlamydomonas reinhardtii (CraCRY) is capable of both, control of transcript levels and the sexual cycle of the alga in a positive (germination) and negative manner (mating ability), as well as catalyzing the repair of UV-DNA lesions. Its 1.6 Å crystal structure shows besides the FAD chromophore an aromatic tetrad that is indispensable in animal-like type I cryptochromes for light-driven change of their signaling-active redox state and formation of a stable radical pair. Given CraCRY’s catalytic activity as (6-4) photolyase in vivo and in vitro, we present the first co-crystal structure of a cryptochrome with duplex DNA comprising a (6-4) pyrimidine–pyrimidone lesion. This 2.9 Å structure reveals a distinct conformation for the catalytic histidine His1, H357, that challenges previous models of a single-photon driven (6-4) photolyase mechanism.

Ultrafast Oxidation of a Tyrosine by Proton-Coupled Electron Transfer Promotes Light Activation of an Animal-like Cryptochrome

“…All these factors are congruent with the unique properties of CraCRY in vivo. 70 ; resolution 1.6 Å). FAD is represented in yellow, the conserved tryptophan triad in green, Y 373 in cyan, D321 in blue and the side tryptophans as reported by Li et al 37 in grey.…”

“…31,40 , we chose to probe WH •+ around 610 nm, expecting under these conditions that essentially a single transition of WH •+ is observed. At this point, it is interesting to compare the experimental anisotropies to predictions based on the crystal structure of WT-CraCRY (PDB entry 5ZM0) 70 and on known directions of the transition dipole moments of FAD ox and WH •+ , as previously described. 31,40 Figure S9), one gets new values listed in Table 3 (line correction), which provide a qualitative idea of the effect of the FAD •contribution on the predictions.…”

“…The proton acceptor is likely to be aspartate D 321 that forms a hydrogen bond with the Y 373 hydroxyl group (3.0 Å; Figure 1A). 70 In the following, we discuss possible reaction mechanisms in the framework of limiting cases of PCET following the classification by Hammes-Schiffer and Stuchebrukhov 64 and Liu et al 86 The reaction pathways considered for CraCRY and our notations are shown in Scheme 1. We note that based on published reduction potentials and pK a values in aqueous solution of the amino acid side chains involved, namely E°(WH 54 pK a (YH + /Y  ) ≈ -2, 60 pK a (YH/Y -) ≈ 9.9, 54 and pK a (DH/D -) = 3.9 87 , the overall PCET reaction would be downhill by 0.07 eV.…”

On the optimal relative orientation of radicals in the cryptochrome magnetic compass

“…The largest anisotropy is seen for WC in DmCry. For the animal-like Cryptochrome from Chlamydomonas reinhardtii (PDB ID: 5ZM0) [77] and the model of the avian cryptochrome 4 [75,76], a smaller anisotropy of 0.16 % and 0.15 % is found, respectively. All other relative orientations yield anisotropies of the order of 0.1 %.…”

Multiple probabilistic models extract features from protein sequence data and resolve functional diversity of very different protein families

“…Moreover, some photolyases can repair ssDNA cyclobutane pyrimidine dimer. The initially proposed functional separation between CRYs and PLs has however gradually started to vanish, as there are now several examples of CPF members exhibiting both functions [13][14][15]. In the last decade, new CPF variants, exhibiting different photobiological properties or functions, have been discovered, changing current views on their evolution [9] and functional diversification [13,14,16,17].…”