Structural model of Dex protein from Penicillium minioluteum and its implications in the mechanism of catalysis.
The DEX gene encodes an extracellular dextranase (EC 3.2.1.11); this enzyme hydrolyzes the alpha(1,6) glucosidic bond contained in dextran to release small isomaltosaccharides. Sequence analysis has revealed only one homologous sequence, CB-8 protein, from Arthrobacter sp., with 30% sequence identity. The secondary structure prediction for Dex was corroborated by circular dichroism measurements. To explore the possibility that Dex protein might adopt a fold similar to any known structure, we conducted a threading search of a three-dimensional structure database. This search revealed that the Dex sequence is compatible with the galactose oxidase/methanol dehydrogenase/sialidase fold. A structural model of Dex based on these results is physically and biologically plausible and leads to testable predictions, including the prediction that Asp246 and Glu299 might be catalytic residues. Also, according to this model the Dex enzyme has a mechanism of hydrolysis with net inversion of anomeric configuration.
Pons
T
T
Centro de Ingeniería Genética y Biotecnología (CIGB), Havana, Cuba. model@CIGB.edu.cu
Chinea
G
G
Olmea
O
O
Beldarraín
A
A
Roca
H
H
Padrón
G
G
Valencia
A
A
D000595:Amino Acid Sequence; D001665:Binding Sites; D002384:Catalysis; D002942:Circular Dichroism; D003910:Dextranase / Q000737:chemistry*; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000737:chemistry*; D005692:Galactose Oxidase / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010406:Penicillins / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D016415:Sequence Alignment; D013329:Structure-Activity Relationship
D005656:Fungal Proteins; D010406:Penicillins; D005692:Galactose Oxidase; D003910:Dextranase