Structure of<i>Bacillus subtilis</i>γ-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue

Ida, Takashi; Suzuki, Hideyuki; Fukuyama, Keiichi; Hiratake, Jun; Wada, Keita

doi:10.1107/s1399004713031222

Cited by 14 publications

(8 citation statements)

References 37 publications

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“…Additionally, acivicin (ACI) is an antineoplastic antibiotic, which was determined to inhibit the enzymatic function of bacterial γ-GT and could be used as the inhibitor of bacterial γ-GT for the imaging experiment. 3,36 The bacterium K. Pneumoniae 1495 was cultured in LB medium to afford enough bacterial cells (10 9 cells/mL). Then, the fluorescent probe ADMG (50 μM) was added into the culture and coincubated for 1 h. The blank group without ADMG and inhibitory group in the presence of ACI (100 μM) were established at the same time.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Isolation of γ-Glutamyl-Transferase Rich-Bacteria from Mouse Gut by a Near-Infrared Fluorescent Probe with Large Stokes Shift

et al. 2018

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Bacterial γ-glutamyltranspeptidases (γ-GT) is a well-known metabolic enzyme, which could cleave the γ-glutamyl amide bond of γ-glutamyl analogues. As a key metabolic enzyme of bacteria and a virulence factor for the host, bacterial γ-GT was determined to be a novel pharmaceutical target for new antibiotics development. However, there is no efficient method for the sensing of γ-GT activity in bacteria and the recognition of γ-glutamyltransferase rich-bacteria. In the present work, a dicyanoisophorone derivative (ADMG) has been designed and developed to be a sensitive and selective near-infrared fluorescent probe for the sensing of bacterial γ-GT. ADMG not only sensed bacterial γ-GT in vitro, but also imaged intestinal bacteria in vivo. More interesting, the intestinal bacteria existed in the duodenum section of mouse displayed significant fluorescence emission. Under the guidance of the sensing of γ-GT using ADMG, three intestinal bacteria strains K. pneumoniae CAV1042, K. pneumoniae XJRML-1, and E. faecalis were isolated successfully, which expressed the bacterial γ-GT. Therefore, the fluorescent probe ADMG not only sensed the endogenous bacterial γ-GT and imaged the intestinal bacteria but also guided the isolation of intestinal bacteria possessing γ-GT efficiently, which suggested a novel biological tool for the rapid isolation of special bacteria from a mixed sample.

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Section: ■ Results and Discussionmentioning

confidence: 99%

Isolation of γ-Glutamyl-Transferase Rich-Bacteria from Mouse Gut by a Near-Infrared Fluorescent Probe with Large Stokes Shift

et al. 2018

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“…The assignment of a C3=N2 double bond is further supported by the hydrogen bonding interaction whereby the Leu420 amide donates to the acceptor N2. We note also that an sp 2 ‐hybridized C3 is assigned in the high‐resolution structure of Bacillus subtilis γ‐glutamyltranspeptidase . In stark contrast an sp 3 ‐hybridized C3 is reported in the structure of the Escherichia coli γ‐glutamyltranspeptidase acivicin adduct .…”

Section: Figurementioning

confidence: 69%

An Improved Model of the Trypanosoma brucei CTP Synthetase Glutaminase Domain–Acivicin Complex

2017

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The natural product acivicin inhibits the glutaminase activity of cytidine triphosphate (CTP) synthetase and is a potent lead compound for drug discovery in the area of neglected tropical diseases, specifically trypanosomaisis. A 2.1‐Å‐resolution crystal structure of the acivicin adduct with the glutaminase domain from Trypanosoma brucei CTP synthetase has been deposited in the RCSB Protein Data Bank (PDB) and provides a template for structure‐based approaches to design new inhibitors. However, our assessment of that data identified deficiencies in the model. We now report an improved and corrected inhibitor structure with changes to the chirality at one position, the orientation and covalent structure of the isoxazoline moiety, and the location of a chloride ion in an oxyanion binding site that is exploited during catalysis. The model is now in agreement with established chemical principles and allows an accurate description of molecular recognition of the ligand and the mode of binding in a potentially valuable drug target.

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“…The first crystal structure to be elucidated was of E. coli GGT (EcGGT) in 2006; in fact, three different structures of EcGGT (PDB IDs: 2DBU, 2D5G, 2DBX) were determined simultaneously (Table 2; Okada et al, 2006). Thereafter, GGT structures from a variety of microbes such as H. pylori (HpGGT), B. subtilis (BsGGT), B. licheniformis (BlGGT), B. anthracis (BanGGT; CapD), Bacillus halodurans (BhGGT), Pseudomonas nitoreducens (PnGGT), and Thermoplasma acidophilum (TaGGT) were determined (Boanca et al, 2007;Okada et al, 2007;Williams et al, 2009; Wu et al, 2009; Wada et al, 2010;Ida et al, 2014;Pica et al, 2016;Kumari et al, 2017; Table 2). Although the mammalian GGTs were the first to be described in detail, heavy glycosylation and membranebound localization made it difficult to determine their structure; the first crystal structure of human GGT was solved in 2013 (West et al, 2013).…”

Section: Structural and Topological Featuresmentioning

confidence: 99%

Bacterial Gamma-Glutamyl Transpeptidase, an Emerging Biocatalyst: Insights Into Structure–Function Relationship and Its Biotechnological Applications

et al. 2021

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Gamma-glutamyl transpeptidase (GGT) enzyme is ubiquitously present in all life forms and plays a variety of roles in diverse organisms. Higher eukaryotes mainly utilize GGT for glutathione degradation, and mammalian GGTs have implications in many physiological disorders also. GGTs from unicellular prokaryotes serve different physiological functions in Gram-positive and Gram-negative bacteria. In the present review, the physiological significance of bacterial GGTs has been discussed categorizing GGTs from Gram-negative bacteria like Escherichia coli as glutathione degraders and from pathogenic species like Helicobacter pylori as virulence factors. Gram-positive bacilli, however, are considered separately as poly-γ-glutamic acid (PGA) degraders. The structure–function relationship of the GGT is also discussed mainly focusing on the crystallization of bacterial GGTs along with functional characterization of conserved regions by site-directed mutagenesis that unravels molecular aspects of autoprocessing and catalysis. Only a few crystal structures have been deciphered so far. Further, different reports on heterologous expression of bacterial GGTs in E. coli and Bacillus subtilis as hosts have been presented in a table pointing toward the lack of fermentation studies for large-scale production. Physicochemical properties of bacterial GGTs have also been described, followed by a detailed discussion on various applications of bacterial GGTs in different biotechnological sectors. This review emphasizes the potential of bacterial GGTs as an industrial biocatalyst relevant to the current switch toward green chemistry.

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Structure ofBacillus subtilisγ-glutamyltranspeptidase in complex with acivicin: diversity of the binding mode of a classical and electrophilic active-site-directed glutamate analogue

Cited by 14 publications

References 37 publications

Isolation of γ-Glutamyl-Transferase Rich-Bacteria from Mouse Gut by a Near-Infrared Fluorescent Probe with Large Stokes Shift

Isolation of γ-Glutamyl-Transferase Rich-Bacteria from Mouse Gut by a Near-Infrared Fluorescent Probe with Large Stokes Shift

An Improved Model of the Trypanosoma brucei CTP Synthetase Glutaminase Domain–Acivicin Complex

Bacterial Gamma-Glutamyl Transpeptidase, an Emerging Biocatalyst: Insights Into Structure–Function Relationship and Its Biotechnological Applications

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