TY - JOUR
T1 - Crystal structure of D-amino acid oxidase
T2 - A case of active site mirror-image convergent evolution with flavocytochrome b2
AU - Mattevi, Andrea
AU - Vanoni, Maria Antonietta
AU - Todone, Flavia
AU - Rizzi, Menico
AU - Teplyakov, Alex
AU - Coda, Alessandro
AU - Bolognesi, Martino
AU - Curti, Bruno
PY - 1996/7/23
Y1 - 1996/7/23
N2 - D-amino acid oxidase is the prototype of the FAD-dependent oxidases. It catalyses the oxidation of D-amino acids to the corresponding α-ketoacids. The reducing equivalents are transferred to molecular oxygen with production of hydrogen peroxide. We have solved the crystal structure of the complex of D-amino acid oxidase with benzoate, a competitive inhibitor of the substrate, by single isomorphous replacement and eightfold averaging. Each monomer is formed by two domains with an overall topology similar to that of p-hydroxybenzoate hydroxylase. The benzoate molecule lays parallel to the flavin ring and is held in position by a salt bridge with Arg-283. Analysis of the active site shows that no side chains are properly positioned to act as the postulated base required for the catalytic carboanion mechanism. On the contrary, the benzoate binding mode suggests a direct transfer of the substrate α-hydrogen to the flavin during the enzyme reductive half-reaction. The active site of D-amino acid oxidase exhibits a striking similarity with that of flavocytochrome b2, a structurally unrelated FMN-dependent flavoenzyme. The active site groups of these two enzymes are in fact superimposable once the mirror-image of the flavocytochrome b2 active site is generated with respect to the flavin plane. Therefore, the catalytic sites of D-amino acid oxidase and flavocytochrome b2 appear to have converged to a highly similar but enantiomeric architecture in order to catalyze similar reactions (oxidation of α-amino acids or α-hydroxy acids), although with opposite stereochemistry.
AB - D-amino acid oxidase is the prototype of the FAD-dependent oxidases. It catalyses the oxidation of D-amino acids to the corresponding α-ketoacids. The reducing equivalents are transferred to molecular oxygen with production of hydrogen peroxide. We have solved the crystal structure of the complex of D-amino acid oxidase with benzoate, a competitive inhibitor of the substrate, by single isomorphous replacement and eightfold averaging. Each monomer is formed by two domains with an overall topology similar to that of p-hydroxybenzoate hydroxylase. The benzoate molecule lays parallel to the flavin ring and is held in position by a salt bridge with Arg-283. Analysis of the active site shows that no side chains are properly positioned to act as the postulated base required for the catalytic carboanion mechanism. On the contrary, the benzoate binding mode suggests a direct transfer of the substrate α-hydrogen to the flavin during the enzyme reductive half-reaction. The active site of D-amino acid oxidase exhibits a striking similarity with that of flavocytochrome b2, a structurally unrelated FMN-dependent flavoenzyme. The active site groups of these two enzymes are in fact superimposable once the mirror-image of the flavocytochrome b2 active site is generated with respect to the flavin plane. Therefore, the catalytic sites of D-amino acid oxidase and flavocytochrome b2 appear to have converged to a highly similar but enantiomeric architecture in order to catalyze similar reactions (oxidation of α-amino acids or α-hydroxy acids), although with opposite stereochemistry.
KW - Density averaging
KW - Flavoenzyme
KW - Redox catalysis
KW - Stereospecificity
UR - http://www.scopus.com/inward/record.url?scp=0029839452&partnerID=8YFLogxK
U2 - 10.1073/pnas.93.15.7496
DO - 10.1073/pnas.93.15.7496
M3 - Article
SN - 0027-8424
VL - 93
SP - 7496
EP - 7501
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
IS - 15
ER -