Stereo-electronic control of reaction selectivity in short-chain dehydrogenases: Decarboxylation, epimerization, and dehydration

Borg, Annika J. E.; Beerens, Koen; Pfeiffer, Martin; Desmet, Tom; Nidetzky, Bernd

doi:10.1016/j.cbpa.2020.09.010

Cited by 17 publications

(48 citation statements)

References 60 publications

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“…The subgroup of SDRs active on NDP-sugars (NS-SDRs) has been found to execute a very diverse range of chemical catalysis, including epimerization (EC 5), dehydration and decarboxylation (both EC 4) and oxidoreduction (EC 1) (Fig. 1.A) (Borg et al, 2021). This functional diversity is noteworthy knowing that they share the same protein fold and that the core catalytic mechanism is driven by two highly conserved residues: a tyrosine serving as Brønsted acid/base for reduction/oxidation and four amino acids distanced to that, a conserved lysine essential for binding the nicotinamide ribose and lowering the tyrosine's hydroxyl pKa (Fig.…”

Section: Introductionmentioning

confidence: 99%

Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering

Costa

Gevaert

Overtveldt

et al. 2021

Biotechnology Advances

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Section: Introductionmentioning

confidence: 99%

Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering

Costa

Gevaert

Overtveldt

et al. 2021

Biotechnology Advances

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“…Nucleotide sugar 6-dehydrogenases include HexNAc-DH and Hex-DH (Figure 2). They all belong to the Short-chain Dehydrogenase Reductase (SDR) superfamily (20). These enzymes catalyze the conversion of hexose / HexNAc to the corresponding uronic acid derivative.…”

Section: Resultsmentioning

confidence: 99%

“…Nucleotide sugar 6-dehydrogenases include HexNAc-DH and Hex-DH (Figure 2). They belong to the Short-chain Dehydrogenase Reductase (SDR) superfamily (Borg et al 2020) and catalyze the conversion of hexose / HexNAc to the corresponding uronic acid. Two profiles, HexNAc-DH HMM and Hex-DH HMM , were built to identify proteins belonging to these two functional families (Figure 1).…”

Section: Resultsmentioning

confidence: 99%

Searching sequence databases for functional homologs using profile HMMs: how to set bit score thresholds?

Srivastava

Hembrom

Kumawat

et al. 2021

Preprint

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UniProt and BFD databases together have 2.5 billion protein sequences. A large majority of these proteins have been electronically annotated. Automated annotation pipelines, vis-à-vis manual curation, have the advantage of scale and speed but are fraught with relatively higher error rates. This is because sequence homology does not necessarily translate to functional homology, molecular function specification is hierarchic and not all functional families have the same amount of experimental data that one can exploit for annotation. Consequently, customization of annotation workflow is inevitable to minimize annotation errors. In this study, we illustrate possible ways of customizing the search of sequence databases for functional homologs using profile HMMs. Choosing an optimal bit score threshold is a critical step in the application of HMMs. We illustrate ways in which an optimal bit score can be arrived at using four Case Studies. These are the single domain nucleotide sugar 6-dehydrogenase and lysozyme-C families, and SH3 and GT-A domains which are typically found as a part of multi-domain proteins. We also discuss the limitations of using profile HMMs for functional annotation and suggests some possible ways to partially overcome such limitations.

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“…The results also showed a small amount of rhamnose produced in polysaccharides of the Brewer’s yeast BY4742-A6180 transformation group, which did not appear in the Brewer’s yeast BY4742 control group, although not as significant as the elevation of galactose. Moreover, PF16363 domain is also contained in UDP-xylose synthase which converts UDP-glucuronic acid into UDP-xylose ( Borg et al, 2021 ).…”

Section: Resultsmentioning

confidence: 99%

Characterization and Heterologous Expression of UDP-Glucose 4-Epimerase From a Hericium erinaceus Mutant with High Polysaccharide Production

Zou

Ren

et al. 2021

Front. Bioeng. Biotechnol.

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Hericium erinaceus is an important medicinal fungus in traditional Chinese medicine because of its polysaccharides and other natural products. Compared terpenoids and polyketides, the analysis of synthetic pathway of polysaccharides is more difficult because of the many genes involved in central metabolism. In previous studies, A6180, encoding a putative UDP-glucose 4-epimerase (UGE) in an H. erinaceus mutant with high production of active polysaccharides, was significantly upregulated. Since there is no reliable genetic manipulation technology for H. erinaceus, we employed Escherichia coli and Saccharomyces cerevisiae to study the function and activity of A6180. The recombinant overexpression vector pET22b-A6180 was constructed for heterologous expression in E. coli. The enzymatic properties of the recombinant protein were investigated. It showed that the recombinant A6180 could strongly convert UDP-α-D-glucose into UDP-α-D-galactose under optimal conditions (pH 6.0, 30°C). In addition, when A6180 was introduced into S. cerevisiae BY4742, xylose was detected in the polysaccharide composition of the yeast transformant. This suggested that the protein coded by A6180 might be a multifunctional enzyme. The generated polysaccharides with a new composition of sugars showed enhanced macrophage activity in vitro. These results indicate that A6180 plays an important role in the structure and activity of polysaccharides. It is a promising strategy for producing polysaccharides with higher activity by introducing A6180 into polysaccharide-producing mushrooms.

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Stereo-electronic control of reaction selectivity in short-chain dehydrogenases: Decarboxylation, epimerization, and dehydration

Cited by 17 publications

References 60 publications

Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering

Structure-function relationships in NDP-sugar active SDR enzymes: Fingerprints for functional annotation and enzyme engineering

Searching sequence databases for functional homologs using profile HMMs: how to set bit score thresholds?

Characterization and Heterologous Expression of UDP-Glucose 4-Epimerase From a Hericium erinaceus Mutant with High Polysaccharide Production

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