Structural insights into the catalytic mechanism of sphingomyelinases D and evolutionary relationship to glycerophosphodiester phosphodiesterases |
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Authors: | Murakami Mário T Fernandes-Pedrosa Matheus Freitas de Andrade Sonia A Gabdoulkhakov Azat Betzel Christian Tambourgi Denise V Arni Raghuvir K |
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Affiliation: | Department of Physics, IBILCE/UNESP, S?o José do Rio Preto-SP, Brazil. |
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Abstract: | Spider venom sphingomyelinases D catalyze the hydrolysis of sphingomyelin via an Mg(2+) ion-dependent acid-base catalytic mechanism which involves two histidines. In the crystal structure of the sulfate free enzyme determined at 1.85A resolution, the metal ion is tetrahedrally coordinated instead of the trigonal-bipyramidal coordination observed in the sulfate bound form. The observed hyperpolarized state of His47 requires a revision of the previously suggested catalytic mechanism. Molecular modeling indicates that the fundamental structural features important for catalysis are fully conserved in both classes of SMases D and that the Class II SMases D contain an additional intra-chain disulphide bridge (Cys53-Cys201). Structural analysis suggests that the highly homologous enzyme from Loxosceles bonetti is unable to hydrolyze sphingomyelin due to the 95Gly-->Asn and 134Pro-->Glu mutations that modify the local charge and hydrophobicity of the interfacial face. Structural and sequence comparisons confirm the evolutionary relationship between sphingomyelinases D and the glicerophosphodiester phosphoesterases which utilize a similar catalytic mechanism. |
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Keywords: | Sphingomyelinase D Catalytic mechanism Mg2+-binding site Hydrodynamic behavior Crystal structure Glycerophosphodiester phosphodiesterases |
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