scholarly journals Molecular Basis of C–S Bond Cleavage in the Glycyl Radical Enzyme Isethionate Sulfite-Lyase

2020 ◽  
Author(s):  
Christopher D. Dawson ◽  
Stephania Irwin ◽  
Lindsey Backman ◽  
Catherine Drennan ◽  
Emily Balskus
Keyword(s):  
Molecular Basis ◽  
Bond Cleavage ◽  
Glycyl Radical ◽  
Glycyl Radical Enzyme

scholarly journals Molecular Basis of C–N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase

2016 ◽  
Vol 23 (10) ◽  
pp. 1206-1216 ◽  
Author(s):  
Smaranda Bodea ◽  
Michael A. Funk ◽  
Emily P. Balskus ◽  
Catherine L. Drennan
Keyword(s):  
Molecular Basis ◽  
Bond Cleavage ◽  
Glycyl Radical ◽  
Glycyl Radical Enzyme

scholarly journals Molecular basis of C-S bond cleavage in the glycyl radical enzyme isethionate sulfite-lyase

2021 ◽  
Author(s):  
Christopher D. Dawson ◽  
Stephania M. Irwin ◽  
Lindsey R.F. Backman ◽  
Chip Le ◽  
Jennifer X. Wang ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Bond Cleavage ◽  
Glycyl Radical ◽  
Glycyl Radical Enzyme

scholarly journals Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme

eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Lindsey RF Backman ◽  
Yolanda Y Huang ◽  
Mary C Andorfer ◽  
Brian Gold ◽  
Ronald T Raines ◽  
...  
Keyword(s):  
Active Site ◽  
Metabolic Pathways ◽  
Molecular Basis ◽  
Radical Mechanism ◽  
Human Gut ◽  
Clostridioides Difficile ◽  
Glycyl Radical ◽  
Biochemical Studies ◽  
Glycyl Radical Enzyme ◽  
Insight Into

The glycyl radical enzyme (GRE) superfamily utilizes a glycyl radical cofactor to catalyze difficult chemical reactions in a variety of anaerobic microbial metabolic pathways. Recently, a GRE, trans-4-hydroxy-L-proline (Hyp) dehydratase (HypD), was discovered that catalyzes the dehydration of Hyp to (S)-Δ1-pyrroline-5-carboxylic acid (P5C). This enzyme is abundant in the human gut microbiome and also present in prominent bacterial pathogens. However, we lack an understanding of how HypD performs its unusual chemistry. Here, we have solved the crystal structure of HypD from the pathogen Clostridioides difficile with Hyp bound in the active site. Biochemical studies have led to the identification of key catalytic residues and have provided insight into the radical mechanism of Hyp dehydration.

Metabolism of Hydrocarbons in n-Alkane-Utilizing Anaerobic Bacteria

2016 ◽  
Vol 26 (1-3) ◽  
pp. 138-151 ◽  
Author(s):  
Heinz Wilkes ◽  
Wolfgang Buckel ◽  
Bernard T. Golding ◽  
Ralf Rabus
Keyword(s):  
Bond Cleavage ◽  
Anaerobic Bacteria ◽  
Sulfate Reducer ◽  
Alkane Degradation ◽  
Carbon Centers ◽  
Glycyl Radical ◽  
Kinetic Isotope ◽  
Dead End ◽  
Bacterium Strain ◽  
Glycyl Radical Enzyme

The glycyl radical enzyme-catalyzed addition of <i>n</i>-alkanes to fumarate creates a C-C-bond between two concomitantly formed stereogenic carbon centers. The configurations of the two diastereoisomers of the product resulting from <i>n</i>-hexane activation by the <i>n</i>-alkane-utilizing denitrifying bacterium strain HxN1, i.e. (1-methylpentyl)succinate, were assigned as (2<i>S</i>,1′<i>R</i>) and (2<i>R</i>,1′<i>R</i>). Experiments with stereospecifically deuterated <i>n</i>-(2,5-<sup>2</sup>H<sub>2</sub>)hexanes revealed that exclusively the pro-<i>S</i> hydrogen atom is abstracted from C2 of the <i>n</i>-alkane by the enzyme and later transferred back to C3 of the alkylsuccinate formed. These results indicate that the alkylsuccinate-forming reaction proceeds with an inversion of configuration at the carbon atom (C2) of the <i>n</i>-alkane forming the new C-C-bond, and thus stereochemically resembles a S<sub>N</sub>2-type reaction. Therefore, the reaction may occur in a concerted manner, which may avoid the highly energetic hex-2-yl radical as an intermediate. The reaction is associated with a significant primary kinetic isotope effect (kH/kD ≥3) for hydrogen, indicating that the homolytic C-H-bond cleavage is involved in the first irreversible step of the reaction mechanism. The (1-methylalkyl)succinate synthases of <i>n</i>-alkane-utilizing anaerobic bacteria apparently have very broad substrate ranges enabling them to activate not only aliphatic but also alkyl-aromatic hydrocarbons. Thus, two denitrifiers and one sulfate reducer were shown to convert the nongrowth substrate toluene to benzylsuccinate and further to the dead-end product benzoyl-CoA. For this purpose, however, the modified β-oxidation pathway known from alkylbenzene-utilizing bacteria was not employed, but rather the pathway used for <i>n</i>-alkane degradation involving CoA ligation, carbon skeleton rearrangement and decarboxylation. Furthermore, various <i>n</i>-alkane- and alkylbenzene-utilizing denitrifiers and sulfate reducers were found to be capable of forming benzyl alcohols from diverse alkylbenzenes, putatively via dehydrogenases. The thermophilic sulfate reducer strain TD3 forms <i>n</i>-alkylsuccinates during growth with <i>n</i>-alkanes or crude oil, which, based on the observed patterns of homologs, do not derive from a terminal activation of <i>n</i>-alkanes.

scholarly journals A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacteriumBilophila wadsworthia

2019 ◽  
Vol 116 (8) ◽  
pp. 3171-3176 ◽  
Author(s):  
Spencer C. Peck ◽  
Karin Denger ◽  
Anna Burrichter ◽  
Stephania M. Irwin ◽  
Emily P. Balskus ◽  
...  
Keyword(s):  
Hydrogen Sulfide ◽  
Bond Cleavage ◽  
Anaerobic Respiration ◽  
Desulfovibrio Desulfuricans ◽  
Intestinal Bacteria ◽  
Differential Proteomics ◽  
Terminal Electron Acceptor ◽  
Glycyl Radical ◽  
Glycyl Radical Enzyme

Hydrogen sulfide (H2S) production in the intestinal microbiota has many contributions to human health and disease. An important source of H2S in the human gut is anaerobic respiration of sulfite released from the abundant dietary and host-derived organic sulfonate substrate in the gut, taurine (2-aminoethanesulfonate). However, the enzymes that allow intestinal bacteria to access sulfite from taurine have not yet been identified. Here we decipher the complete taurine desulfonation pathway inBilophila wadsworthia3.1.6 using differential proteomics, in vitro reconstruction with heterologously produced enzymes, and identification of critical intermediates. An initial deamination of taurine to sulfoacetaldehyde by a known taurine:pyruvate aminotransferase is followed, unexpectedly, by reduction of sulfoacetaldehyde to isethionate (2-hydroxyethanesulfonate) by an NADH-dependent reductase. Isethionate is then cleaved to sulfite and acetaldehyde by a previously uncharacterized glycyl radical enzyme (GRE), isethionate sulfite-lyase (IslA). The acetaldehyde produced is oxidized to acetyl-CoA by a dehydrogenase, and the sulfite is reduced to H2S by dissimilatory sulfite reductase. This unique GRE is also found inDesulfovibrio desulfuricansDSM642 andDesulfovibrio alaskensisG20, which use isethionate but not taurine; corresponding knockout mutants ofD. alaskensisG20 did not grow with isethionate as the terminal electron acceptor. In conclusion, the novel radical-based C-S bond-cleavage reaction catalyzed by IslA diversifies the known repertoire of GRE superfamily enzymes and enables the energy metabolism ofB. wadsworthia. This GRE is widely distributed in gut bacterial genomes and may represent a novel target for control of intestinal H2S production.

scholarly journals Author response: Molecular basis for catabolism of the abundant metabolite trans-4-hydroxy-L-proline by a microbial glycyl radical enzyme

2020 ◽  
Author(s):  
Lindsey RF Backman ◽  
Yolanda Y Huang ◽  
Mary C Andorfer ◽  
Brian Gold ◽  
Ronald T Raines ◽  
...  
Keyword(s):  
Molecular Basis ◽  
Author Response ◽  
Glycyl Radical ◽  
Glycyl Radical Enzyme
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