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

Abstract

The Short‐chain Dehydrogenases/Reductases Engineering Database (SDRED) covers one of the largest known protein families (168 150 proteins). Assignment to the superfamilies of Classical and Extended SDRs was achieved by global sequence similarity and by identification of family‐specific sequence motifs. Two standard numbering schemes were established for Classical and Extended SDRs that allow for the determination of conserved amino acid residues, such as cofactor specificity determining positions or superfamily specific sequence motifs. The comprehensive sequence dataset of the SDRED facilitates the refinement of family‐specific sequence motifs. The glycine‐rich motifs for Classical and Extended SDRs were refined to improve the precision of superfamily classification. In each superfamily, the majority of sequences formed a tightly connected sequence network and belonged to a large homologous family. Despite their different sequence motifs and their different sequence length, the two sequence networks of Classical and Extended SDRs are not separate, but connected by edges at a threshold of 40% sequence similarity, indicating that all SDRs belong to a large, connected network. The SDRED is accessible at https://sdred.biocatnet.de/.

Systematic Evaluation of Imine‐Reducing Enzymes: Common Principles in Imine Reductases, β‐Hydroxy Acid Dehydrogenases, and Short‐Chain Dehydrogenases/ Reductases

“…[18] Despite their promiscuous imine-reducing activity, these members of the SDR family have no significant global sequence similarity to IREDs. [19] Although the catalytic mechanism of IREDs is not completely understood, [20] it is assumed that protonation of the imine occurs in the catalytic site. [21] The resulting iminium is then reduced by a hydride transferred from NAD(P)H. [22] Two superfamilies have been distinguished: the R-and the S-selective IREDs.…”

Crossing the Border: From Keto‐ to Imine Reduction in Short‐Chain Dehydrogenases/Reductases

“…The structure of Zt _SDR was solved in complex with NADP + and compared well to the structure of NR (see the Supporting Information); however, a substrate or inhibitor could not be co‐crystallized thus far. The alanine scan revealed that next to the SDR‐typical catalytic triad (positions S144, Y159, K163 according to the standard numbering scheme for “classical” SDRs), three proton‐donor flanking residues Y100, C150, H158 (standard positions 96, 146, 156) mediate imine reduction . This pattern was extended by polar residues that are common in the substrate binding site of NR and Zt _SDR (N102, C149, T/S199; standard positions 98, 145, 197), but do not occur at the equivalent positions in Ao _SDR (T124, I171, V221).…”

“…To confirm the functional relevance of the flanking and consensus positions (Figure , Table ), an in silico screening for SDRs with imine‐reducing activity was performed assuming a similar structure of “classical” SDRs even at low sequence identity . Therefore, the Short‐Chain Dehydrogenase/Reductase Engineering Database was scanned separately for sequences with tyrosine, asparagine, cysteine, cysteine, histidine, or threonine/serine at standard positions 96, 98, 145, 146, 156, or 197, respectively. Interestingly, none of the 130000 SDR sequences had more than three matching positions.…”

Bioconversion of Biologically Active Indole Derivatives with Indole-3-Acetic Acid-Degrading Enzymes from Caballeronia glathei DSM50014

“…IacE possesses a Rossman fold domain, strongly indicating a redox function of this enzyme. Also, according to the SDRED database [47], IacE belongs to the HFAM1 family of the classical short-chain dehydrogenases/reductases. All major structural motifs of this family can be identified in the sequence of IacE (Supplementary Figure S21): four active site residues (Asn111, Ser139, Tyr153, and Lys157), NNAG motif, stabilizing the central β-sheet (Asn96, Asn97, Ala98, Gly99), a glycine-rich motif for the binding of NAD(P)H (9ThrGlyAlaAlaArgGlyLeuGly16) and PG motif (Pro193, Gly194).…”