Crystal structure of a lipase from <i>Streptomyces</i> sp. strain W007 – implications for thermostability and regiospecificity

Zhao, Zhongyang; Hou, Shulin; Lan, Dongming; Wang, Xiumei; Liu, Jinsong; Khan, Faez Iqbal; Wang, Yonghua

doi:10.1111/febs.14211

Cited by 49 publications

(46 citation statements)

References 46 publications

(74 reference statements)

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“…The knowledge of protein three-dimensional (3D) structures are vital for rational drug design (Stephens et al, 2014 ; Khan et al, 2017a ; Lan et al, 2017 ; Zhao et al, 2017 ). The 3D structure of RhlR was predicted using homology.…”

Section: Methodsmentioning

confidence: 99%

Seed Extract of Psoralea corylifolia and Its Constituent Bakuchiol Impairs AHL-Based Quorum Sensing and Biofilm Formation in Food- and Human-Related Pathogens

Husain

Ahmad

Khan

et al. 2018

Front. Cell. Infect. Microbiol.

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The emergence of multi-drug resistance in pathogenic bacteria in clinical settings as well as food-borne infections has become a serious health concern. The problem of drug resistance necessitates the need for alternative novel therapeutic strategies to combat this menace. One such approach is targeting the quorum-sensing (QS) controlled virulence and biofilm formation. In this study, we first screened different fractions of Psoralea corylifolia (seed) for their anti-QS property in the Chromobacterium violaceum 12472 strain. The methanol fraction was found to be the most active fraction and was selected for further bioassays. At sub-inhibitory concentrations, the P. corylifolia methanol fraction (PCMF) reduced QS-regulated virulence functions in C. violaceum CVO26 (violacein); Pseudomonas aeruginosa (elastase, protease, pyocyanin, chitinase, exopolysaccharides (EPS), and swarming motility), A. hydrophila (protease, EPS), and Serratia marcescens (prodigiosin). Biofilm formation in all the test pathogens was reduced significantly (p ≤ 0.005) in a concentration-dependent manner. The β-galactosidase assay showed that the PCMF at 1,000 μg/ml downregulated las-controlled transcription in PAO1. In vivo studies with C. elegans demonstrated increased survival of the nematodes after treatment with the PCMF. Bakuchiol, a phytoconstituent of the extract, demonstrated significant inhibition of QS-regulated violacein production in C. violaceum and impaired biofilm formation in the test pathogens. The molecular docking results suggested that bakuchiol efficiently binds to the active pockets of LasR and RhlR, and the complexes were stabilized by several hydrophobic interactions. Additionally, the molecular dynamics simulation of LasR, LasR–bakuchiol, RhlR, and RhlR–bakuchiol complexes for 50 ns revealed that the binding of bakuchiol to LasR and RhlR was fairly stable. The study highlights the anti-infective potential of the PCMF and bakuchiol instead of bactericidal or bacteriostatic action, as the extract targets QS-controlled virulence and the biofilm.

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Section: Methodsmentioning

confidence: 99%

Seed Extract of Psoralea corylifolia and Its Constituent Bakuchiol Impairs AHL-Based Quorum Sensing and Biofilm Formation in Food- and Human-Related Pathogens

Husain

Ahmad

Khan

et al. 2018

Front. Cell. Infect. Microbiol.

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“…Figure 7A). Among the remaining 29 CEH structures, 16 belong to various architectures, but 13 CEHs (representative PDB codes: 4V95 [134], 5AH1 [100], 5GMX [61], 5H3B [62], 5H6B [102], 5UGQ [40], 5XPX, 5YAL [160], 6A12 [103], 6AAE [63], 6EHN [41], 6GRY [42] and 6QGB [177]) are not classified under the CATH database classification. Secreted PLA2 from S. violaceoruber (PDB code: 1LWB) forms an up-down bundle structure with only helices ( Figure 7B).…”

Section: Classification Based On Tertiary Structurementioning

confidence: 99%

“…2QUA [86], 2QUB [86], 2QXT [87], 2QXU [87], 2W22 [88], 2Z5G [80], 2Z8X [89], 2Z8Z [89], 2ZJ6 [90], 2ZJ7 [90], 2ZVD [91], 3A6Z [91], 3A70 [91], 3AUK, 3D2A [92], 3D2B [92], 3D2C [92], 3LIP [83], 3QMM [93], 3QZU [94], 3UMJ [95], 3W9U, 4FDM [96], 4FKB, 4FMP, 4GW3 [97], 4GXN [97], 4HS9 [97], 4LIP [98], 4OPM, 4X6U [99], 4X71 [99], 4X7B [99], 4X85 [99], 5AH1 [100], 5CE5 [100], 5CRI [101], 5CT4 [101], 5CT6 [101], 5CT9 [101], 5CTA [101], 5CUR [101], 5H6B [102], 5LIP [98], 5MAL 2 [39], 5XPX, 6A12 [103], 6CL4 [103], 6FZ1 [104], 6FZ7 [104], 6FZ8 [104], 6FZ9 [104], 6FZA [104], 6FZC …”

Section: Introductionmentioning

confidence: 99%

Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application

Kim

2019

Crystals

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Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from 52 genera and metagenome have been reported. In this review, we categorize these structures based on catalytic machinery, structure and substrate specificity to provide a comprehensive understanding of the bacterial CEHs. CEHs use Ser, Asp or water as a nucleophile to drive diverse catalytic machinery. The α/β/α sandwich architecture is most frequently found in CEHs, but 3-solenoid, β-barrel, up-down bundle, α/β/β/α 4-layer sandwich, 6 or 7 propeller and α/β barrel architectures are also found in these CEHs. Most are substrate-specific to various esters with types of head group and lengths of the acyl chain, but some CEHs exhibit peptidase or lactamase activities. CEHs are widely used in industrial applications, and are the objects of research in structure- or mutation-based protein engineering. Structural studies of CEHs are still necessary for understanding their biological roles, identifying their structure-based functions and structure-based engineering and their potential industrial applications.

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“…However, none of the enzymes exhibited an enantioselectivity high enough for efficient kinetic resolution (Figures S56 and S57). Currently, protein engineering of the lipase Streptomyces sp . is ongoing to obtain a more enantioselective and hence, practical catalyst.…”

Section: Methodsmentioning

confidence: 99%

“…Currently,p rotein engineering of the lipase Streptomyces sp. [16] is ongoing to obtainamore enantioselectivea nd hence, practical catalyst. Finally,w ei nvestigated the possibility of performingh aloetherification reactions in the currents etup.…”

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confidence: 99%

Chemoenzymatic Halocyclization of γ,δ‐Unsaturated Carboxylic Acids and Alcohols

et al. 2019

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Crystal structure of a lipase from Streptomyces sp. strain W007 – implications for thermostability and regiospecificity

Abstract: Structural data are available in the Protein Data Bank database under the accession numbers 5H6B and 5H6G.

Cited by 49 publications

References 46 publications

Seed Extract of Psoralea corylifolia and Its Constituent Bakuchiol Impairs AHL-Based Quorum Sensing and Biofilm Formation in Food- and Human-Related Pathogens

Seed Extract of Psoralea corylifolia and Its Constituent Bakuchiol Impairs AHL-Based Quorum Sensing and Biofilm Formation in Food- and Human-Related Pathogens

Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application

Chemoenzymatic Halocyclization of γ,δ‐Unsaturated Carboxylic Acids and Alcohols

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