Decoding transaminase motifs: Tracing the unknown patterns for enhancing the accuracy of computational screening...

Area of Science:

• Biochemistry and Enzymology
• Bioinformatics and Computational Biology

Background:

• Transaminases are vital enzymes with four subfamilies: D-alanine transaminase (DATA), L-selective Branched chain aminotransferase (BCAT), 4-amino-4-deoxychorismate lyase (ADCL), and R-selective aminotransferase (RATA).
• RATA enzymes are highly valuable for biocatalysis, particularly in synthesizing chiral amines and resolving racemic mixtures.
• Identifying RATA enzymes is challenging due to the lack of effective motif-based screening methods in sequence databases.

Purpose of the Study:

• To construct a comprehensive transaminase sequence dataset and categorize enzymes into their respective subfamilies.
• To screen for conserved and novel motifs within these transaminase subfamilies.
• To validate the functional and structural importance of identified motifs using phylogenetic clustering and structural localization on predicted protein models.

Main Methods:

• Dataset construction and subfamily categorization of transaminases.
• Screening for conserved and novel motifs across ADCL, BCAT, DATA, and RATA subfamilies.
• Phylogenetic analysis and structural localization of motifs on Alphafold-predicted protein models.

Main Results:

• Identification of 5, 7, 10, and 2 novel motifs for ADCL, BCAT, DATA, and RATA, respectively.
• Localization of 3, 5, 7, and 2 motifs on secondary structures, confirming their structural significance.
• Discovery of unique residue patterns, such as 293-KxxxR-297, that can improve computational screening accuracy.

Conclusions:

• The identified novel motifs and conserved residue patterns are crucial for understanding transaminase function.
• A motif-based computational approach can significantly improve the screening and discovery of novel RATA enzymes.
• This research facilitates the exploitation of RATA enzymes in various biocatalytic applications, including chiral amine synthesis.