The ω‐transaminase engineering database (oTAED): A navigation tool in protein sequence and structure space

Abstract

The ω-Transaminase Engineering Database (oTAED) was established as a publicly accessible resource on sequences and structures of the biotechnologically relevant ω-transaminases (ω-TAs) from Fold types I and IV. The oTAED integrates sequence and structure data, provides a classification based on fold type and sequence similarity, and applies a standard numbering scheme to identify equivalent positions in homologous proteins. The oTAED includes 67 210 proteins (114 655 sequences) which are divided into 169 homologous families based on global sequence similarity. The 44 and 39 highly conserved positions which were identified in Fold type I and IV, respectively, include the known catalytic residues and a large fraction of glycines and prolines in loop regions, which might have a role in protein folding and stability. However, for most of the conserved positions the function is still unknown. Literature information on positions that mediate substrate specificity and stereoselectivity was systematically examined. The standard numbering schemes revealed that many positions which have been described in different enzymes are structurally equivalent. For some positions, multiple functional roles have been suggested based on experimental data in different enzymes. The proposed standard numbering schemes for Fold type I and IV ω-TAs assist with analysis of literature data, facilitate annotation of ω-TAs, support prediction of promising mutation sites, and enable navigation in ω-TA sequence space. Thus, it is a useful tool for enzyme engineering and the selection of novel ω-TA candidates with desired biochemical properties.

The scale-free nature of protein sequence space

“…By assuming that evolution has reached an equilibrium in protein sequence space, the more evolvable folds might have become densely populated as a consequence of convergent evolution [ 42 ], thus connecting the concept of hubs to the concept of evolvability. The observation of a uniform distribution of sequences from thermophilic and hyperthermophilic sources in the oTA network demonstrated that hub sequences are not characterized by increased thermostability ( S2 Fig in [ 43 ]).…”

Enantiomer discrimination in β-phenylalanine degradation by a newly isolated Paraburkholderia strain BS115 and type strain PsJN

“…Since activity has only been observed in growing cells, a cofactor-dependent mechanism is likely. Moreover, an additional transaminase would have been detected under the given conditions, and also a side activity of the identified ( S )-β-PA can be excluded: ( R ) and ( S )-ω-TAs show only low sequence identities and can clearly be differentiated by protein fold types (Höhne et al 2010 ; Buß et al 2018a ). A transamination of ( R )-β-PA would have led to the formation of AP, but on the contrary the concentration of AP decreased.…”

The Short‐chain Dehydrogenase/Reductase Engineering Database (SDRED): A classification and analysis system for a highly diverse enzyme family

“…A standard numbering scheme was established for Classical and Extended SDRs to facilitate the identification of structurally and functionally equivalent positions, as it had been previously shown for other enzyme families . Crystal structures were selected to cover mostly all homologous families of Classical and Extended SDRs in the SDRED with known PDB entries.…”

“…Protein family databases are useful tools to study the relationship between sequence, structure, and function of enzymes and to support the design of novel enzymes . In this study, the Short‐chain Dehydrogenase/Reductase Engineering Database ( https://sdred.biocatnet.de/ .)…”