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A similar active site for non–specific and specific endonucleases

Nature Structural Biology volume 6, pages 112–113 (1999)Cite this article

Superposition of the active site residues His 98 and Asn 119 of I– PpoI and His 89 and Asn 119 of Serratia nuclease revealed a structural similarity (r.m.s. deviation of 0.52 Å for the side chain atoms). Moreover, the architectures of the active site regions involving residues Thr 93–Asn 119 in I–PpoI and Lys 84–Asn 119 in the Serratia nuclease are also very similar with an r.m.s. deviation of 1.14 Å for the main chain atoms of 23 residues. Furthermore, the positions of the guanidinium groups from catalytically important Arg residues (Arg 61 in I–PpoI and Arg 57 in the Serratia nuclease) are in similar spatial positions, with respect to the His and Asn residues. In the co–crystal structure of I–PpoI with its reaction products, Arg 61 contacts the 5'–phosphate, and Arg 57 has been shown by a mutational analysis in the Serratia nuclease to be essential for catalysis. From the structural comparison and the published biochemical data we propose that both enzymes share a common catalytic mechanism. In this mechanism His acts as a general base to activate the water. In the structure of I–PpoI bound to its homing sites, His 98 is located such that it could position a water molecule for an in–line attack on the phosphodiester bond that will be cleaved. It is suggested that a water molecule, from the hydration sphere of the Mg2+ ion bound to Asn, protonates the leaving group. For the Serratia nuclease it has been shown that the metal ion cofactor directly contacts the oxygen of Asn 119 (Miller, M.D. and Krause, K.L. unpublished data). The Arg residue (Arg 61 in I–PpoI and Arg 57 in Serratia nuclease) could serve to stabilize the transition state.

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Figure 1: Comparison of I–PpoI and Serratia nuclease.

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Acknowledgements

This work was supported by the Deutsche Forschungsgemeinschaft.

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Authors and Affiliations

  1. Institut für Biochemie (FB 15), Justus–Liebig–Universität Giessen, Heinrich–Buff–Ring 58, Giessen, 35392, Germany

    Peter Friedhoff, Ingo Franke, Gregor Meiss, Wolfgang Wende & Alfred Pingoud

  2. Department of Biochemistry and Biophysical Sciences, University of Houston, Houston, 77204–5934, Texas, USA

    Kurt L. Krause

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  1. Peter Friedhoff
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  2. Ingo Franke
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Correspondence to Alfred Pingoud.

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Friedhoff, P., Franke, I., Meiss, G. et al. A similar active site for non–specific and specific endonucleases . Nat Struct Mol Biol 6, 112–113 (1999). https://doi.org/10.1038/5796

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