A (6-4)-photolyase from the Antarctic bacterium Sphingomonas sp. UV9: recombinant production and in silico features
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ORIGINAL PAPER
A (6‑4)‑photolyase from the Antarctic bacterium Sphingomonas sp. UV9: recombinant production and in silico features Juan José Marizcurrena1 · Tilman Lamparter2 · Susana Castro‑Sowinski1,3 Received: 23 July 2020 / Accepted: 7 September 2020 © Springer Japan KK, part of Springer Nature 2020
Abstract Photolyases are proteins that enzymatically repair the UV-induced DNA damage by a protein–DNA electron transfer mechanism. They repair either cyclobutane pyrimidine dimers or pyrimidine (6-4) pyrimidone photoproducts or just (6-4)-photoproducts. In this work, we report the production and partial characterization of a recombinant (6-4)-photolyase (SphPhrB97) from a bacterial psychrotolerant Antarctic isolate identified as Sphingomonas sp. strain UV9. The spectrum analysis and the in silico study of SphPhrB97 suggest that this enzyme has similar features as compared to the (6-4)-photolyase from Agrobacterium tumefaciens (4DJA; PhrB), including the presence of three cofactors: FAD, DMRL (6,7-dimethyl-8-(1′-D-ribityl) lumazine), and an Fe–S cluster. The homology model of SphPhrB97 predicts that the DNA-binding pocket (area and volume) is larger as compared to (6-4)-photolyases from mesophilic microbes. Based on sequence comparison and on the homology model, we propose an electron transfer pathway towards the FAD cofactor involving the residues Trp342, Trp390, Tyr40, Tyr391, and Tyr399. The phylogenetic tree performed using curated and well-characterized prokaryotic (6-4)-photolyases suggests that SphPhrB97 may have an ancient evolutionary origin. The results suggest that SphPhrB97 is a cold-adapted enzyme, ready to cope with the UV irradiation stress found in a hostile environment, such as Antarctica. Keywords Photolyase · Antarctica · Sphingomonas · DNA damage · (6-4)-photoproduct · Photo repair
Introduction Photolyases (EC 4.1.99.3) are monomeric flavoproteins that harbor chromophores and enzymatically repair the UVinduced DNA damage (formation of DNA photoproducts) by an intraprotein electron transfer mechanism (Zhong 2015; Communicated by A. Driessen. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00792-020-01202-z) contains supplementary material, which is available to authorized users. * Juan José Marizcurrena [email protected]; [email protected] 1
Biochemistry and Molecular Biology, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
2
Botanical Institute, Karlsruhe Institute for Technology, Fritz Haber Weg 4, 76131 Karlsruhe, Germany
3
Laboratory of Hydrolytic Enzymes, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
Kavakli et al. 2019). The chromophores are i) a non‐covalently bound flavin adenine dinucleotide (FAD) cofactor, and ii) a photoantenna that can absorb blue light photons and transfer the energy to the FAD, which, as far, can be MTHF (methyltetrahydrofolate), DMRL (6,7-dimethyl-8(1′-D-ribityl) lumazine), 8-HDF (8-hydroxy-5-deazaflavin), or
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