Active site promiscuity in the S1-P1 nuclease family

T. Kovaľ1, J. Lehmbeck2, A. Noergaard2, L. H. Oestergaard2, J. Stránský1, 3, K. Fejfarová1, P. Kolenko1, J. Dušková1, T. Skálová1, L. Švecová1, 3, M. Trundová1, J. Hašek1 and J. Dohnálek1

1Institute of Biotechnology CAS, v.v.i., Biocev, Průmyslová 595, Vestec, 252 42 Jesenice u Prahy, Czech Republic

2Novozymes A/S, Brudelysvej 26, DK-2880 Bagsværd, Denmark

3Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University, Břehová 7, 115 19 Praha 1, Czech Republic

Members of the S1-P1 nuclease family (Pfam PF02265) play important roles (e.g. scavenging of nutrients, specific apoptotic functions, and pathogen/symbiont – host interactions) in fungi, plants, single cell eukaryotes and some bacteria. Usually they are α-helical proteins with a trinuclear Zn2+ cluster in the center of the surface groove. The fold is stabilized by two or more disulfide bridges. Several oligosaccharides bonded on the surface serve primarily as a shielding of the hydrophobic regions and therefore contribute to solubility and stability. These enzymes act as phosphodiesterases cleaving the bond between phosphorus and the 3’ hydroxyl group. Hydrolysis of the phosphodiester bond is performed by a nucleophilic attack of the activated water (hydroxide) molecule followed by creation of a penta-coordinated transition state and its breakup into the products. Members of this family are either bifunctional (cleave both single stranded and double stranded forms of DNA and RNA) or single strand-specific. All the studied members of this family have also the 3’-nucleotidase activity.

The active site of the S1-P1 nuclease family members is composed of two distinctive parts. The catalytic zinc cluster is responsible for binding of the phosphate moieties. An adjacent pocket serves as a nucleobase binding site. Ligand binding is also affected by the amino acids in close proximity of the active site. Even though structures of three members of the S1-P1 nuclease family are known [1, 2, 3], these structures contain only few ligands in the active site. Our study of a fungal nuclease significantly broadens our understanding of the ligand binding properties of this family and shows the active site flexibility and existence of yet unexpected binding modes.

This work is supported by the project „BIOCEV – Biotechnology and Biomedicine Centre of the Academy of Sciences and Charles University (CZ.1.05/1.1.00/02.0109), from the ERDF and by the Ministry of Education, Youth and Sports of the Czech Republic (grant No. LG14009).

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3.  Yu, T., Maestre-Reyna, M., Ko, C., Ko, T., Sun, Y., Lin, T., Shaw, J., Wang, A.H., Plos One 9, (2014), 05821