Correction to Analysis of the Structure and Function of YfcG from <i>Escherichia coli</i> Reveals an Efficient and Unique Disulfide Bond Reductase

Wadington, Megan C.; Ladner, Jane E.; Stourman, Nina V.; Harp, Joel M.; Armstrong, Richard N.

doi:10.1021/bi101851x

Cited by 5 publications

(16 citation statements)

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“…Nu-class GSTs are found in many organisms ( 16 , 18 ), but their physiological roles are largely unknown. Several Nu-class GSTs have been tested for activity in vitro ; most, including EcYfcG and EcYghU from Escherichia coli , showed disulfide bond reductase activity toward small molecules, such as 2-hydroxyethyl disulfide ( 16 – 18 , 21 ), which led to the proposal that this is their main physiological activity. A strain of E. coli in which the yfcG gene was deleted was impaired in its response to oxidative stress, leading to the proposal that EcYfcG may naturally function as a peroxidase, although this enzyme exhibited low in vitro peroxidase activity with model peroxides ( 22 ).…”

Section: Introductionmentioning

confidence: 99%

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin

Kontur

Bingman

Olmsted

et al. 2018

Journal of Biological Chemistry

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As a major component of plant cell walls, lignin is a potential renewable source of valuable chemicals. Several sphingomonad bacteria have been identified that can break the β-aryl ether bond connecting most phenylpropanoid units of the lignin heteropolymer. Here, we tested three sphingomonads predicted to be capable of breaking the β-aryl ether bond of the dimeric aromatic compound guaiacylglycerol-β-guaiacyl ether (GGE) and found that Novosphingobium aromaticivorans metabolizes GGE at one of the fastest rates thus far reported. After the ether bond of racemic GGE is broken by replacement with a thioether bond involving glutathione, the glutathione moiety must be removed from the resulting two stereoisomers of the phenylpropanoid conjugate β-glutathionyl-γ-hydroxypropiovanillone (GS-HPV). We found that the Nu-class glutathione S-transferase NaGSTNu is the only enzyme needed to remove glutathione from both (R)- and (S)-GS-HPV in N. aromaticivorans. We solved the crystal structure of NaGSTNu and used molecular modeling to propose a mechanism for the glutathione lyase (deglutathionylation) reaction in which an enzyme-stabilized glutathione thiolate attacks the thioether bond of GS-HPV, and the reaction proceeds through an enzyme-stabilized enolate intermediate. Three residues implicated in the proposed mechanism (Thr51, Tyr166, and Tyr224) were found to be critical for the lyase reaction. We also found that Nu-class GSTs from Sphingobium sp. SYK-6 (which can also break the β-aryl ether bond) and Escherichia coli (which cannot break the β-aryl ether bond) can also cleave (R)- and (S)-GS-HPV, suggesting that glutathione lyase activity may be common throughout this widespread but largely uncharacterized class of glutathione S-transferases.

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Section: Introductionmentioning

confidence: 99%

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin

Kontur

Bingman

Olmsted

et al. 2018

Journal of Biological Chemistry

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“…We found 4,149 and 3,259 in KEGG and MetaCyc, respectively. We also added 64 substrates from the literature, − for the total of 6,738 unique substrates.…”

Section: Methodsmentioning

confidence: 99%

Prediction of Substrates for Glutathione Transferases by Covalent Docking

Dong

Calhoun

Fan

et al. 2014

J. Chem. Inf. Model.

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Enzymes in the glutathione transferase (GST) superfamily catalyze the conjugation of glutathione (GSH) to electrophilic substrates. As a consequence they are involved in a number of key biological processes, including protection of cells against chemical damage, steroid and prostaglandin biosynthesis, tyrosine catabolism, and cell apoptosis. Although virtual screening has been used widely to discover substrates by docking potential noncovalent ligands into active site clefts of enzymes, docking has been rarely constrained by a covalent bond between the enzyme and ligand. In this study, we investigate the accuracy of docking poses and substrate discovery in the GST superfamily, by docking 6738 potential ligands from the KEGG and MetaCyc compound libraries into 14 representative GST enzymes with known structures and substrates using the PLOP program [15048827Proteins200455351]. For X-ray structures as receptors, one of the top 3 ranked models is within 3 Å all-atom root mean square deviation (RMSD) of the native complex in 11 of the 14 cases; the enrichment LogAUC value is better than random in all cases, and better than 25 in 7 of 11 cases. For comparative models as receptors, near-native ligand–enzyme configurations are often sampled but difficult to rank highly. For models based on templates with the highest sequence identity, the enrichment LogAUC is better than 25 in 5 of 11 cases, not significantly different from the crystal structures. In conclusion, we show that covalent docking can be a useful tool for substrate discovery and point out specific challenges for future method improvement.

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“…The members of the GST superfamily (>13000 nonredundant members in the cytosolic GST superfamily) catalyze a diverse range of redox reactions as well as conjugation reactions in xenobiotic metabolism. − The canonical GST superfamily members are composed of an N-terminal domain that has a thioredoxin-like fold and a C-terminal domain that has a unique α-helical fold; the active sites are located at the domain interface. An alternate fold in which the thioredoxin-like domain is interrupted by the α-helical domain is also found in eukaryotes and prokaryotes. , This fold represents the so-called kappa GSTs, another superfamily in the thioredoxin fold class whose members catalyze the GST reaction. , The canonical superfamily harbors members that have robust disulfide bond oxidoreductase activity; , these enzymes likely utilize proteins as substrates, thereby extending the challenge of functional prediction to protein–protein interactions. The GST superfamily was selected for inclusion in the EFI because a large number of its diverse members have not been characterized with respect to the boundaries among sequence, structure, and function.…”

Section: Efi: Bridging Projectsmentioning

confidence: 99%

“…28,29 This fold represents the so-called kappa GSTs, another superfamily in the thioredoxin fold class whose members catalyze the GST reaction. 30,31 The canonical superfamily harbors members that have robust disulfide bond oxidoreductase activity; 32,33 these enzymes likely utilize proteins as substrates, thereby extending the challenge of functional prediction to protein−protein interactions. The GST superfamily was selected for inclusion in the EFI because a large number of its diverse members have not been characterized with respect to the boundaries among sequence, structure, and function.…”

Section: ■ Efi: Bridging Projectsmentioning

confidence: 99%

The Enzyme Function Initiative

et al. 2011

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The Enzyme Function Initiative (EFI) was recently established to address the challenge of assigning reliable functions to enzymes discovered in bacterial genome projects; in this Current Topic we review the structure and operations of the EFI. The EFI includes the Superfamily/Genome, Protein, Structure, Computation, and Data/Dissemination Cores that provide the infrastructure for reliably predicting the in vitro functions of unknown enzymes. The initial targets for functional assignment are selected from five functionally diverse superfamilies (amidohydrolase, enolase, glutathione transferase, haloalkanoic acid dehalogenase, and isoprenoid synthase), with five superfamily-specific Bridging Projects experimentally testing the predicted in vitro enzymatic activities. The EFI also includes the Microbiology Core that evaluates the in vivo context of in vitro enzymatic functions and confirms the functional predictions of the EFI. The deliverables of the EFI to the scientific community include: 1) development of a large-scale, multidisciplinary sequence/structure-based strategy for functional assignment of unknown enzymes discovered in genome projects (target selection, protein production, structure determination, computation, experimental enzymology, microbiology, and structure-based annotation); 2) dissemination of the strategy to the community via publications, collaborations, workshops, and symposia; 3) computational and bioinformatic tools for using the strategy; 4) provision of experimental protocols and/or reagents for enzyme production and characterization; and 5) dissemination of data via the EFI’s website, enzymefunction.org. The realization of multidisciplinary strategies for functional assignment will begin to define the full metabolic diversity that exists in nature and will impact basic biochemical and evolutionary understanding, as well as a wide range of applications of central importance to industrial, medicinal and pharmaceutical efforts.

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Correction to Analysis of the Structure and Function of YfcG from Escherichia coli Reveals an Efficient and Unique Disulfide Bond Reductase

Cited by 5 publications

References 0 publications

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin

Novosphingobium aromaticivorans uses a Nu-class glutathione S-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin

Prediction of Substrates for Glutathione Transferases by Covalent Docking

The Enzyme Function Initiative

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