BioCatNet: A Database System for the Integration of Enzyme Sequences and Biocatalytic Experiments. (22nd September 2016)

• Record Type: Journal Article
• Authors: Buchholz, Patrick C. F.; Vogel, Constantin; Reusch, Waldemar; Pohl, Martina; Rother, Dörte; Spieß, Antje C.; Pleiss, Jürgen
• Is Part Of: Chembiochem. Volume 17:Number 21(2016)
• Page Start: 2093
• Page End: 2098
• Publication Date: 2016-09-22
• Subjects: biocatalysis -- data management -- enzymes -- kinetics -- protein design -- sequence-function relationship; Biochemistry -- Periodicals; Molecular biology -- Periodicals; Pharmaceutical chemistry -- Periodicals; 572
• DOI: 10.1002/cbic.201600462
• Languages: English
• ISSNs: 1439-4227

Abstract

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). Abstract : Bringing it all together : The BioCatNet database system integrates enzyme sequences and biocatalytic data (reaction conditions, time‐course of substrates and products). It facilitates long‐term storage and exchange of experimental data between research groups. BioCatNet is a valuable tool for data mining, reaction engineering, and enzyme design.