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Proteins. 2018 May;86(5):566-580. doi: 10.1002/prot.25477. Epub 2018 Mar 5.

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

Author information

1
Institute of Process Engineering in Life Sciences, Karlsruhe Institute of Technology, Engler-Bunte-Ring 3, Karlsruhe, 76131, Germany.
2
Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, Stuttgart, 70569, Germany.

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.

KEYWORDS:

BioCatNet; PLP-dependent enzymes; fold type I; fold type IV; standard numbering scheme

PMID:
29423963
DOI:
10.1002/prot.25477

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