The Crystal Structure of l-Sorbose Reductase from Gluconobacter frateurii Complexed with NADPH and l-Sorbose

Kubota, Keiko; Nagata, Koji; Okai, Masahiko; Miyazono, Ken-ichi; Soemphol, Wichai; Ohtsuka, Jun; Yamamura, Akihiro; Saichana, Natsaran; Toyama, Hirohide; Matsushita, Kazunobu; Tanokura, Masaru

doi:10.1016/j.jmb.2011.01.008

Cited by 17 publications

(8 citation statements)

References 34 publications

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“…Based on previous studies on NADPH‐dependent reductases (Kubota et al ., ; Matsumoto et al ., ; Schiebel et al ., ) and our structural and mutagenesis analyses, we propose a catalytic mechanism of AcuI for acryloyl‐CoA reduction (Fig. C).…”

Section: Resultsmentioning

confidence: 97%

Mechanistic insight into acrylate metabolism and detoxification in marine dimethylsulfoniopropionate‐catabolizing bacteria

Wang

Cao

Chen

et al. 2017

Molecular Microbiology

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SummaryDimethylsulfoniopropionate (DMSP) cleavage, yielding dimethyl sulfide (DMS) and acrylate, provides vital carbon sources to marine bacteria, is a key component of the global sulfur cycle and effects atmospheric chemistry and potentially climate. Acrylate and its metabolite acryloyl-CoA are toxic if allowed to accumulate within cells. Thus, organisms cleaving DMSP require effective systems for both the utilization and detoxification of acrylate. Here, we examine the mechanism of acrylate utilization and detoxification in Roseobacters. We propose propionate-CoA ligase (PrpE) and acryloyl-CoA reductase (AcuI) as the key enzymes involved and through structural and mutagenesis analyses, provide explanations of their catalytic mechanisms. In most cases, DMSP lyases and DMSP demethylases (DmdAs) have low substrate affinities, but AcuIs have very high substrate affinities, suggesting that an effective detoxification system for acylate catabolism exists in DMSP-catabolizing Roseobacters. This study provides insight on acrylate metabolism and detoxification and a possible explanation for the high K m values that have been noted for some DMSP lyases.Since acrylate/acryloyl-CoA is probably produced by other metabolism, and AcuI and PrpE are conserved in many organisms across all domains of life, the detoxification system is likely relevant to many metabolic processes and environments beyond DMSP catabolism.

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Section: Resultsmentioning

confidence: 97%

Mechanistic insight into acrylate metabolism and detoxification in marine dimethylsulfoniopropionate‐catabolizing bacteria

Wang

Cao

Chen

et al. 2017

Molecular Microbiology

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“…The specificity for NADP(H) or NAD(H) is a consequence of the electrostatics in the cofactor binding site. NADP(H)‐dependent SDRs have a conserved arginine or lysine at the C‐cap of the second β‐strand (β2), while NAD(H)‐dependent SDRs are proposed to display negatively charged residues instead, which was assessed by SDR variants . The majority of Classical SDRs have been described to favor NADP(H), while most Extended SDRs prefer NAD(H) .…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2019

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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/.

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“…More recently, an asparagine residue or a histidine residue at the corresponding position was added to the catalytic triad (Filling et al 2002; Kubota et al 2011), since a water molecule bound to the main-chain carbonyl group of the asparagine or histidine is assumed to participate in the reductive reaction. The configuration of these catalytic tetrad residues is well superimposed on that of RrQR (Figure 3a), and thus the catalytic reaction would be achieved through the same proton relay (Filling et al 2002).…”

Section: Resultsmentioning

confidence: 99%

Structural basis of stereospecific reduction by quinuclidinone reductase

et al. 2014

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Chiral molecule (R)-3-quinuclidinol, a valuable compound for the production of various pharmaceuticals, is efficiently synthesized from 3-quinuclidinone by using NADPH-dependent 3-quinuclidinone reductase (RrQR) from Rhodotorula rubra. Here, we report the crystal structure of RrQR and the structure-based mutational analysis. The enzyme forms a tetramer, in which the core of each protomer exhibits the α/β Rossmann fold and contains one molecule of NADPH, whereas the characteristic substructures of a small lobe and a variable loop are localized around the substrate-binding site. Modeling and mutation analyses of the catalytic site indicated that the hydrophobicity of two residues, I167 and F212, determines the substrate-binding orientation as well as the substrate-binding affinity. Our results revealed that the characteristic substrate-binding pocket composed of hydrophobic amino acid residues ensures substrate docking for the stereospecific reaction of RrQR in spite of its loose interaction with the substrate.

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The Crystal Structure of l-Sorbose Reductase from Gluconobacter frateurii Complexed with NADPH and l-Sorbose

Cited by 17 publications

References 34 publications

Mechanistic insight into acrylate metabolism and detoxification in marine dimethylsulfoniopropionate‐catabolizing bacteria

Mechanistic insight into acrylate metabolism and detoxification in marine dimethylsulfoniopropionate‐catabolizing bacteria

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

Structural basis of stereospecific reduction by quinuclidinone reductase

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