X-ray structure and characterization of a thermostable lipase from Geobacillus thermoleovorans

Moharana, Tushar Ranjan; Pal, Biswajit; Rao, Nalam Madhusudhana

doi:10.1016/j.bbrc.2018.11.105

Cited by 19 publications

(11 citation statements)

References 33 publications

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“…The active sites of 5M mutant lipase composed of Ser113, His358, and Aps317. A similar composition of the catalytic triad was found in the crystal structure of Geobacillus thermoleovorans lipase [36]. Both molecules in the asymmetric unit were highly similar, and the superimposition of alpha carbon atoms gave a root-mean-square deviation (RMSD) of 0.7789 Å (Fig 5).…”

Section: Overall Structure Of 5m Lipasesupporting

confidence: 63%

Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae

et al. 2021

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5M mutant lipase was derived through cumulative mutagenesis of amino acid residues (D43E/T118N/E226D/E250L/N304E) of T1 lipase from Geobacillus zalihae. A previous study revealed that cumulative mutations in 5M mutant lipase resulted in decreased thermostability compared to wild-type T1 lipase. Multiple amino acids substitution might cause structural destabilization due to negative cooperation. Hence, the three-dimensional structure of 5M mutant lipase was elucidated to determine the evolution in structural elements caused by amino acids substitution. A suitable crystal for X-ray diffraction was obtained from an optimized formulation containing 0.5 M sodium cacodylate trihydrate, 0.4 M sodium citrate tribasic pH 6.4 and 0.2 M sodium chloride with 2.5 mg/mL protein concentration. The three-dimensional structure of 5M mutant lipase was solved at 2.64 Å with two molecules per asymmetric unit. The detailed analysis of the structure revealed that there was a decrease in the number of molecular interactions, including hydrogen bonds and ion interactions, which are important in maintaining the stability of lipase. This study facilitates understanding of and highlights the importance of hydrogen bonds and ion interactions towards protein stability. Substrate specificity and docking analysis on the open structure of 5M mutant lipase revealed changes in substrate preference. The molecular dynamics simulation of 5M-substrates complexes validated the substrate preference of 5M lipase towards long-chain p-nitrophenyl–esters.

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Section: Overall Structure Of 5m Lipasesupporting

confidence: 63%

Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae

et al. 2021

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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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“…Interestingly, the only case where the DSSP and STRIDE servers performed better than PRAS was the assignment of turn, and this is due primarily to the fact that turn is the least abundant of the three secondary structure elements and the CD technique is less sensitive to its occurrence. Moreover, many researchers associate turn with other structures such as β-bridge and bend (e.g., the experimental study 28 that estimated secondary structure elements of lipase associated turn with random structures).…”

Section: Assessing the Replacement Of Hydrogen Atomsmentioning

confidence: 99%

Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions

Nnyigide

Lee

et al. 2022

J. Chem. Inf. Model.

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The Protein Data Bank (PDB) file format developed at Brookhaven National Laboratory is the most popular file format to store biological data and is widely supported by many software programs for the editing and visualization of macromolecular structures. Unfortunately, many of these structures have variety of issues ranging from missing side chains and/or atoms to alternate locations (rotamers). To fix these flaws, one has to learn a new program, compile modules, and install libraries. To overcome these challenges, we present Protein Repair and Analysis Server (PRAS), an easy-to-use web server to repair protein structures and add missing atoms. The PRAS program flow has two main sections. In the first section, several subroutines are called to deal with sequence microheterogeneity, rotamers, missing side chains, heavy atoms, or hydrogen atoms. A log file is generated detailing irregularities and their fixes as carried out by the program. In the later section, the program uses the error-corrected protein structure to assign secondary structure elements based on amide-amide interactions of the backbone. Plots of four Ramachandran types (general, glycine, proline, and pre-proline) and percentage of secondary structure elements; a log file and the error-corrected PDB file can be downloaded by clicking on the download link generated by the server. The server is freely available and is accessed through its web address at . Alternatively, users can download the source code from the server or install the program on their local machines following the instructions at or . While the present work focuses on the repair of structural data in the PDB format, the server is capable of fixing similar errors in the extensible and newly adopted mmCIF format.

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X-ray structure and characterization of a thermostable lipase from Geobacillus thermoleovorans

Cited by 19 publications

References 33 publications

Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae

Structure elucidation and docking analysis of 5M mutant of T1 lipase Geobacillus zalihae

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

Protein Repair and Analysis Server: A Web Server to Repair PDB Structures, Add Missing Heavy Atoms and Hydrogen Atoms, and Assign Secondary Structures by Amide Interactions

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