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Chembiochem. 2016 Nov 3;17(21):2093-2098. doi: 10.1002/cbic.201600462. Epub 2016 Sep 22.

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

Author information

1
Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
2
IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
3
Institute of Biochemical Engineering, Technical University of Braunschweig, Rebenring 56, 38106, Braunschweig, Germany.
4
RWTH Aachen University, AVT.EPT, Worringerweg 1, 52074, Aachen, Germany.
5
Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany. Juergen.Pleiss@itb.uni-stuttgart.de.

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).

KEYWORDS:

biocatalysis; data management; enzymes; kinetics; protein design; sequence-function relationship

PMID:
27562499
DOI:
10.1002/cbic.201600462
[Indexed for MEDLINE]

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