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3D Structure-Guided Screening

Enzyme discovery based on 3D structure of proteins is a great complement to the sole analysis of the primary sequence, since sequence-based methods often lead to the discovery of enzymes belonging to already known families. In addition, the primary structure, amino acid sequence, is not always correlated to certain 3D structures, while enzyme functions are mainly determined by its 3D structure. Therefore, searching only by sequence often results in undesired activity or misses the target enzyme.

A lot of effort has been made to develop bioinformatic tools to predict the function of a protein from its 3D structures, which constitutes a broadened resource for novel enzyme discovery. Databases such as Protein Data Bank index the 3D structural data of biological macromolecules. Furthermore, databases providing catalytic residue annotation specifically for enzymes were also built.

An approach based on overall 3D structures can be undertaken for enzymes belonging to families or sub-families for which at least one member has a solved structure. For example, four synthetic structures for which no function was known were identified by Steffen-Munsberg et al. as useful transaminases by evaluating the active region. Also, discovery of enzymes can be conducted by focusing on highly conserved regions associated with catalysis, including catalytic residues, cofactor and substrate binding residues and their relative spatial positions forming the minimal catalytic active site constellation. This method allowed Steinkellner et al. to identify two promiscuous reductases (Old Yellow Enzyme, OYE), having completely different sequence and fold compared to typical OYEs.

Creative Enzymes has rich experience to provide 3D structure-guided strategies for novel enzyme discovery. We help to develop strategies for custom assignments of proteins with unknown functions, in order to provide a better understanding of metabolism and enzymology from a fundamental perspective. With years of experience of combining different techniques in enzyme discovery, we offer professional one-stop services:

Searching for new enzymes by 3D structure The 3D structure of Plasmepsin II.

References

Related sections

Sequence-based Screening



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