Structural insights into the catalytic mechanism of sphingomyelinases D and evolutionary relationship to glycerophosphodiester phosphodiesterases.
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.
Murakami
Mário T
MT
Department of Physics, IBILCE/UNESP, São José do Rio Preto-SP, Brazil.
Fernandes-Pedrosa
Matheus Freitas
MF
de Andrade
Sonia A
SA
Gabdoulkhakov
Azat
A
Betzel
Christian
C
Tambourgi
Denise V
DV
Arni
Raghuvir K
RK
D000595:Amino Acid Sequence; D001665:Binding Sites; D002384:Catalysis; D002413:Cations, Divalent / Q000737:chemistry; D018360:Crystallography, X-Ray; D019143:Evolution, Molecular; D006860:Hydrogen Bonding; D008274:Magnesium / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry* / Q000145:classification / Q000235:genetics / Q000378:metabolism*; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D040681:Structural Homology, Protein
D002413:Cations, Divalent; D010727:Phosphoric Diester Hydrolases; C055160:sphingomyelin phosphodiesterase D; C038133:glycerophosphodiester phosphodiesterase; D008274:Magnesium