scholarly journals Structure guided engineering of a cold active esterase expands substrate range though a stabilisation mutation that allows access to a buried water chamber

2021 ◽  
Author(s):  
Nehad Noby ◽  
Rachel L. Johnson ◽  
Jonathan D. Tyzack ◽  
Amira M. Embaby ◽  
Hesham Saeed ◽  
...  

AbstractCold active esterases represent an important class of enzymes capable of undertaking useful chemical transformations at low temperatures. EstN7 from Bacillus cohnii represents a true psychrophilic esterase with a temperature optimum below 20°C. We have recently determined the structure of EstN7 and have used this knowledge to understand substrate specificity and expands its substrate range through protein engineering. Substrate range is determined by a plug at the end of acyl binding pocket that blocks access to a buried water filled cavity, so limiting EstN7 to turnover of C2 and C4 substrates. Data mining revealed a potentially important commercial reaction, conversion of triacetin to only the 1,2-glyceryl diacetate isomer, which the EstN7 was capable of achieving. Residues M187, N211 and W206 were identified as plug residues. M187 was identified as the key plug residue but mutation to alanine destabilised the structure as whole. Another plug mutation, N211A had a stabilising effect on EstN7 and suppressed the destabilising M187A mutation. The M187A-N211A variant had the broadest substrate range, capable of hydrolysing a C8 substrate. Thus, the structure of EstN7 together with focused engineering has provided new insights into the structural stability and substrate specificity that allowed expansion of substrate range.

2019 ◽  
Vol 8 (6) ◽  
pp. 1325-1336 ◽  
Author(s):  
Naazneen Sofeo ◽  
Jason H. Hart ◽  
Brandon Butler ◽  
David J. Oliver ◽  
Marna D. Yandeau-Nelson ◽  
...  

Nematology ◽  
2002 ◽  
Vol 4 (8) ◽  
pp. 925-932 ◽  
Author(s):  
Rodney Edmondson ◽  
Paul Richardson ◽  
Deena Willmott ◽  
Andrew Hart ◽  
Steve Long

AbstractThe susceptibility of overwintering black vine weevil larvae Otiorhynchus sulcatus to a cold-active entomopathogenic nematode, Steinernema kraussei (isolate L137) and a commercial proprietary biopesticide, Steinernema carpocapsae (Exhibit) was assessed on outdoor potted strawberry plants. Nematodes were applied at a range of doses in early winter at a field site located in Warwickshire, England. Three months later, infestation and mortality of vine weevils were assessed. There was a clear dose response observed for S. kraussei applications. Up to 81% of vine weevil control was recorded by this nematode at the highest dose of 60 000 nematodes per pot, whereas treatments with S. carpocapsae caused no significant mortality at the dose rates used. Dissection of vine weevil larvae showed infective juveniles had developed to adults within the host. Recovery of nematodes at the end of the experiment indicated that S. kraussei (L137) was able to survive winter field conditions including prolonged exposure to low temperatures (averaging 2.7°C during the experiment) in contrast to S. carpocapsae which showed poor survival. Of the two extraction methods used, the Baermann funnel technique was found to be more efficient than Galleria mellonella baiting, with up to 44% of the original highest dose of S. kraussei nematodes being recovered by Baermann funnel compared to 8% with G. mellonella at 18°C. These results suggest S. kraussei (L137) has potential as a commercial biocontrol agent against O. sulcatus at low temperatures.


Catalysts ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 747
Author(s):  
Samah Hashim Albayati ◽  
Malihe Masomian ◽  
Siti Nor Hasmah Ishak ◽  
Mohd Shukuri bin Mohamad Ali ◽  
Adam Leow Thean ◽  
...  

Microbial lipases represent one of the most important groups of biotechnological biocatalysts. However, the high-level production of lipases requires an understanding of the molecular mechanisms of gene expression, folding, and secretion processes. Stable, selective, and productive lipase is essential for modern chemical industries, as most lipases cannot work in different process conditions. However, the screening and isolation of a new lipase with desired and specific properties would be time consuming, and costly, so researchers typically modify an available lipase with a certain potential for minimizing cost. Improving enzyme properties is associated with altering the enzymatic structure by changing one or several amino acids in the protein sequence. This review detailed the main sources, classification, structural properties, and mutagenic approaches, such as rational design (site direct mutagenesis, iterative saturation mutagenesis) and direct evolution (error prone PCR, DNA shuffling), for achieving modification goals. Here, both techniques were reviewed, with different results for lipase engineering, with a particular focus on improving or changing lipase specificity. Changing the amino acid sequences of the binding pocket or lid region of the lipase led to remarkable enzyme substrate specificity and enantioselectivity improvement. Site-directed mutagenesis is one of the appropriate methods to alter the enzyme sequence, as compared to random mutagenesis, such as error-prone PCR. This contribution has summarized and evaluated several experimental studies on modifying the substrate specificity of lipases.


2018 ◽  
Author(s):  
Richard Nemeth ◽  
Mackenzie Neubert ◽  
Thomas Ni ◽  
Christopher J. Ackerson

In the present work we have identified a glutathione reductase like metalloid reductase (GRLMR) responsible for mediating selenite tolerance in <i>Pseudomonas moravenis</i> stanleyae through the enzymatic generation of Se(0) nanoparticles. This enzyme has an unprecedented substrate specificity for selenodiglutathione (K<sub>m</sub>= 336 μM) over oxidized glutathione (K<sub>m</sub>=8.22 mM). This enzyme was able to induce selenite tolerance in foreign bacterial cell lines by increasing the IC<sub>90</sub> for selenite from 1.9 mM in cell lacking the GRLMR gene to 21.3 mM for cells containing the GRLMR gene. It was later confirmed by STEM and EDS that Se nanoparticles were absent in control cells and present in cells expressing GRLMR. Structural analysis suggests the lack of a sulfur residue in the substrate/product binding pocket may be responsible for this unique substrate specificity.


2019 ◽  
Vol 476 (22) ◽  
pp. 3475-3492 ◽  
Author(s):  
Robert D. Grinshpon ◽  
Suman Shrestha ◽  
James Titus-McQuillan ◽  
Paul T. Hamilton ◽  
Paul D. Swartz ◽  
...  

Apoptotic caspases evolved with metazoans more than 950 million years ago (MYA), and a series of gene duplications resulted in two subfamilies consisting of initiator and effector caspases. The effector caspase genes (caspases-3, -6, and -7) were subsequently fixed into the Chordata phylum more than 650 MYA when the gene for a common ancestor (CA) duplicated, and the three effector caspases have persisted throughout mammalian evolution. All caspases prefer an aspartate residue at the P1 position of substrates, so each caspase evolved discrete cellular roles through changes in substrate recognition at the P4 position combined with allosteric regulation. We examined the evolution of substrate specificity in caspase-6, which prefers valine at the P4 residue, compared with caspases-3 and -7, which prefer aspartate, by reconstructing the CA of effector caspases (AncCP-Ef1) and the CA of caspase-6 (AncCP-6An). We show that AncCP-Ef1 is a promiscuous enzyme with little distinction between Asp, Val, or Leu at P4. The specificity of caspase-6 was defined early in its evolution, where AncCP-6An demonstrates a preference for Val over Asp at P4. Structures of AncCP-Ef1 and of AncCP-6An show a network of charged amino acids near the S4 pocket that, when combined with repositioning a flexible active site loop, resulted in a more hydrophobic binding pocket in AncCP-6An. The ancestral protein reconstructions show that the caspase-hemoglobinase fold has been conserved for over 650 million years and that only three substitutions in the scaffold are necessary to shift substrate selection toward Val over Asp.


Antibiotics ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1494
Author(s):  
Jenifer Cuesta Bernal ◽  
Jasmin El-Delik ◽  
Stephan Göttig ◽  
Klaas M. Pos

Gram-negative Tripartite Resistance Nodulation and cell Division (RND) superfamily efflux pumps confer various functions, including multidrug and bile salt resistance, quorum-sensing, virulence and can influence the rate of mutations on the chromosome. Multidrug RND efflux systems are often characterized by a wide substrate specificity. Similarly to many other RND efflux pump systems, AcrAD-TolC confers resistance toward SDS, novobiocin and deoxycholate. In contrast to the other pumps, however, it in addition confers resistance against aminoglycosides and dianionic β-lactams, such as sulbenicillin, aztreonam and carbenicillin. Here, we could show that AcrD from Salmonella typhimurium confers resistance toward several hitherto unreported AcrD substrates such as temocillin, dicloxacillin, cefazolin and fusidic acid. In order to address the molecular determinants of the S. typhimurium AcrD substrate specificity, we conducted substitution analyses in the putative access and deep binding pockets and in the TM1/TM2 groove region. The variants were tested in E. coli ΔacrBΔacrD against β-lactams oxacillin, carbenicillin, aztreonam and temocillin. Deep binding pocket variants N136A, D276A and Y327A; access pocket variant R625A; and variants with substitutions in the groove region between TM1 and TM2 conferred a sensitive phenotype and might, therefore, be involved in anionic β-lactam export. In contrast, lower susceptibilities were observed for E. coli cells harbouring deep binding pocket variants T139A, D176A, S180A, F609A, T611A and F627A and the TM1/TM2 groove variant I337A. This study provides the first insights of side chains involved in drug binding and transport for AcrD from S. typhimurium.


2016 ◽  
Author(s):  
Joshua M. Lubner ◽  
George M. Church ◽  
Michael F. Chou ◽  
Daniel Schwartz

Protein kinase specificity is largely imparted through substrate binding pocket motifs. Missense mutations in these regions are frequently associated with human disease, and in some cases can alter substrate specificity. However, current efforts at decoding the influence of mutations on substrate specificity have been focused on disease-associated mutations. Here, we adapted the Proteomic Peptide Library (ProPeL) approach for determining kinase specificity to the task of exploring structure-function relationships in kinase specificity by interrogating the effects of synthetic mutation. We established a specificity model for the wild-type DYRK1A kinase with unprecedented resolution. Using existing crystallographic and sequence homology data, we rationally designed mutations that precisely reprogrammed the DYRK1A kinase at the P+1 position to mimic the substrate preferences of a related kinase, CK II. This study illustrates a new synthetic biological approach to reprogram kinase specificity by design, and a powerful new paradigm to investigate structure-function relationships underpinning kinase substrate specificity.


2015 ◽  
Vol 357 (12) ◽  
pp. 2712-2720 ◽  
Author(s):  
Sang-Woo Han ◽  
Eul-Soo Park ◽  
Joo-Young Dong ◽  
Jong-Shik Shin

Author(s):  
Mitja Lenic ◽  
Peter Kokol ◽  
Petra Povalej ◽  
Milan Zorman

The aggressive rate of growth of disk storage and, thus, the ability to store enormous quantities of data have far outpaced our ability to process and utilize that. This challenge has produced a phenomenon called data tombs—data is deposited to merely rest in peace, never to be accessed again. But the growing appreciation that data tombs represent missed opportunities in cases supporting scientific discovering, business exploitation, or complex decision making has awakened the growing commercial interest in knowledge discovery and data-mining techniques. That, in order, has stimulated new interest in the automatic knowledge induction from cases stored in large databases—a very important class of techniques in the data-mining field. With the variety of environments, it is almost impossible to develop a single-induction method that would fit all possible requirements. Thereafter, we constructed a new so-called multi-method approach, trying out some original solutions.


1994 ◽  
Vol 49 (3-4) ◽  
pp. 163-170 ◽  
Author(s):  
Birgit Fuchs ◽  
Petra Suttner ◽  
Sabine Sterner ◽  
Robert Wastlhuber ◽  
Eckhard Loos

D-Enzyme (4-a-glucanotransferase, EC 2.4.1.25) from cultured symbiotic Nostoc and Chlorella has been partially purified and characterized. The enzyme catalyzes the disproportionation of maltooligosaccharides and is able to form maltooligosaccharides from soluble starch and D-glucose. The properties of D-enzyme from Nostoc and Chlorella are similar with respect to substrate specificity, KM values and pH dependence, but differ with respect to temperature optimum and molecular weight (40 °C/50 kDa and 50 °C/230 kDa for the enzyme from Nostoc and Chlorella, respectively). D-enzyme activity has been demonstrated also in freeliving Anabaena, Chlorella and Chlamydomonas. Its physiological role in symbiotic Nostoc is briefly discussed


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