BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments

Abstract

The development of novel enzymes for biocatalytic processes requires knowledge on substrate profile and selectivity; this can be derived from databases and from publications. Often, these sources lack time-course data for the substrate or product, and an unambiguous link between experiment and enzyme sequence. The lack of integrated, original data hampers the comprehensive analysis of enzyme kinetics and the evaluation of sequence-function relationships. In order to accelerate enzyme engineering, BioCatNet integrates protein sequence, protein structure, and experimental data for a given enzyme family. BioCatNet explicitly assigns the enzyme sequence to the experimental data, which consists of information on reaction conditions and time-course data. BioCatNet facilitates the consistent documentation of reaction conditions, the archiving of time-course data, and the efficient exchange of experimental data among collaborators. Data integration is demonstrated for three case studies by using the TEED (Thiamine diphosphate-dependent Enzymes Engineering Database).

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

“…The Short‐chain Dehydrogenase/Reductase Engineering Database (SDRED) was established within our in‐house data warehouse system . It integrates data on protein sequences and structures and provides tools for extraction, transformation, and loading of data from publicly available databases.…”

Towards a Mechanistic Understanding of Factors Controlling the Stereoselectivity of Transketolase

“…The previously developed Thiamine diphosphate dependent Enzyme Engineering Database (TEED, https://teed.biocatnet.de) was used as repository for experiments within the BioCatNet database system to archive both reaction conditions and measurement results. [31,52] As tandard numbering scheme was established to unambiguously annotate positions and mutation sites for the superfamily of TKs as described previously for ThDP-dependent DCs. [15] In total, 16 crystal structures were selected from different species with known TK structures ( Supplementary Table S3).…”

“…The goal of this study was to understand factors controlling stereoselectivity in TKs and to develop an extended model that includes DCs and TKs starting from published data on different TKs, specifically concerning the carboligation of non‐phosphorylated substrates. For the better comparison of data, a standard numbering scheme for TK sequences is presented and available as annotation in the Thiamine diphosphate‐dependent Enzyme Engineering Database (TEED) (https://teed.biocatnet.de) …”

“…For the betterc omparison of data, as tandard numbering scheme for TK sequences is presented and available as annotation in the Thiamine diphosphate-de-pendentE nzyme Engineering Database (TEED)( https://teed.biocatnet.de). [31] The stereoselectivity model for TKs was evaluated using the carboligation of 3-hydroxypyruvate(1)a sadonor and n-pentanal (2a)a nd propanal (2b)a sa cceptors ( Figure 2B), as for those substrates several TK variants with altered stereoselectivity have been described andt he hydrophobic side chains of the aliphatic acceptor substrates will not form stabilising inter- Figure 1. Extendedf our-state stereoselectivity model for ThDP-dependent enzymes.The model was extended from two to four binding states prior to CÀCbond formation that are definedb yt he orientation of the acceptorside chain relative to the donor side chain and by the orientationo ft he acceptor carbonyl group relative to the ThDP-bound donor hydroxy group.…”

Harnessing plant metabolic diversity

“…Numerous databases and consortia exist that collate information about enzyme families and their functions (e.g. the Carbohydrate-Active Enzymes database [17], the Cytochrome P450 Homepage [18], BioCatNet [19]), transcriptome databases for medicinal plants [1,2], and for linking known metabolic and chemical diversity with medicinal and/or industrial relevance and the wider academic literature (e.g. KNApSAcK for cataloguing bioactivities [20], and PubChem [21,22], Reaxys® [23] and SciFinder®[24] for recording the reported chemical space and results from biological assays).…”