Fine-tuning of the substrate binding mode to enhance the catalytic efficiency of an ortho-haloacetophenone-specific carbonyl reductase

2020 ◽  
Vol 10 (8) ◽  
pp. 2462-2472
Author(s):  
Aipeng Li ◽  
Xue Li ◽  
Wei Pang ◽  
Qing Tian ◽  
Ting Wang ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Catalytic Efficiency ◽  
Binding Mode ◽  
Carbonyl Reductase ◽  
Fine Tuning

Fine-tuning of the substrate binding mode was successfully applied for enhancing the catalytic efficiency of an ortho-haloacetophenone-specific carbonyl reductase.

Fine-tuning dirhodium compounds with bridging ligands: Synthesis, structure, catalytic efficiency

2021 ◽  
Vol 954-955 ◽  
pp. 122078
Author(s):  
Yangbo Ning ◽  
Jiantao Tan ◽  
Zhifan Wang ◽  
Yuanhua Wang
Keyword(s):  
Catalytic Efficiency ◽  
Fine Tuning ◽  
Bridging Ligands

scholarly journals Improving the Substrate Affinity and Catalytic Efficiency of β-Glucosidase Bgl3A from Talaromyces leycettanus JCM12802 by Rational Design

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1882
Author(s):  
Wei Xia ◽  
Yingguo Bai ◽  
Pengjun Shi
Keyword(s):  
Hydrogen Bonding ◽  
Rational Design ◽  
Substrate Binding ◽  
Enzymatic Saccharification ◽  
Catalytic Efficiency ◽  
Binding Pocket ◽  
Glycoside Hydrolases ◽  
Cellulosic Biomass ◽  
Substrate Affinity ◽  
Hydrogen Bonding Networks

Improving the substrate affinity and catalytic efficiency of β-glucosidase is necessary for better performance in the enzymatic saccharification of cellulosic biomass because of its ability to prevent cellobiose inhibition on cellulases. Bgl3A from Talaromyces leycettanus JCM12802, identified in our previous work, was considered a suitable candidate enzyme for efficient cellulose saccharification with higher catalytic efficiency on the natural substrate cellobiose compared with other β-glucosidase but showed insufficient substrate affinity. In this work, hydrophobic stacking interaction and hydrogen-bonding networks in the active center of Bgl3A were analyzed and rationally designed to strengthen substrate binding. Three vital residues, Met36, Phe66, and Glu168, which were supposed to influence substrate binding by stabilizing adjacent binding site, were chosen for mutagenesis. The results indicated that strengthening the hydrophobic interaction between stacking aromatic residue and the substrate, and stabilizing the hydrogen-bonding networks in the binding pocket could contribute to the stabilized substrate combination. Four dominant mutants, M36E, M36N, F66Y, and E168Q with significantly lower Km values and 1.4–2.3-fold catalytic efficiencies, were obtained. These findings may provide a valuable reference for the design of other β-glucosidases and even glycoside hydrolases.

scholarly journals The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release

2018 ◽  
Vol 293 (21) ◽  
pp. 7969-7981 ◽  
Author(s):  
Thomas E. Bohl ◽  
Pek Ieong ◽  
John K. Lee ◽  
Thomas Lee ◽  
Jayakanth Kankanala ◽  
...  
Keyword(s):  
Rational Design ◽  
Substrate Binding ◽  
Flexible Substrate ◽  
Binding Mode ◽  
Antibiotic Development ◽  
Product Release ◽  
Outer Leaflet ◽  
Hydrogen Deuterium ◽  
Dynamics Simulations ◽  
Secondary Membrane

Gram-negative bacteria are surrounded by a secondary membrane of which the outer leaflet is composed of the glycolipid lipopolysaccharide (LPS), which guards against hydrophobic toxins, including many antibiotics. Therefore, LPS synthesis in bacteria is an attractive target for antibiotic development. LpxH is a pyrophosphatase involved in LPS synthesis, and previous structures revealed that LpxH has a helical cap that binds its lipid substrates. Here, crystallography and hydrogen–deuterium exchange MS provided evidence for a highly flexible substrate-binding cap in LpxH. Furthermore, molecular dynamics simulations disclosed how the helices of the cap may open to allow substrate entry. The predicted opening mechanism was supported by activity assays of LpxH variants. Finally, we confirmed biochemically that LpxH is inhibited by a previously identified antibacterial compound, determined the potency of this inhibitor, and modeled its binding mode in the LpxH active site. In summary, our work provides evidence that the substrate-binding cap of LpxH is highly dynamic, thus allowing for facile substrate binding and product release between the capping helices. Our results also pave the way for the rational design of more potent LpxH inhibitors.

Predictable Selectivity in Remote C−H Oxidation of Steroids: Analysis of Substrate Binding Mode

2020 ◽  
Vol 59 (31) ◽  
pp. 12703-12708 ◽  
Author(s):  
Giorgio Olivo ◽  
Giorgio Capocasa ◽  
Barbara Ticconi ◽  
Osvaldo Lanzalunga ◽  
Stefano Di Stefano ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Binding Mode

Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode

2020 ◽  
Vol 527 (3) ◽  
pp. 799-804
Author(s):  
Shuyu Zhou ◽  
Tzu-Ping Ko ◽  
Jian-Wen Huang ◽  
Weidong Liu ◽  
Yingying Zheng ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Binding Mode ◽  
Metabolizing Enzyme

A Nitrogenase Cluster Model [Fe8S6O] with an Oxygen Unsymmetrically Bridging Two Proto-Fe4S3 Cubes: Relevancy to the Substrate Binding Mode of the FeMo Cofactor

2012 ◽  
Vol 51 (21) ◽  
pp. 11217-11219 ◽  
Author(s):  
Shun Ohta ◽  
Yasuhiro Ohki ◽  
Takayoshi Hashimoto ◽  
Roger E. Cramer ◽  
Kazuyuki Tatsumi
Keyword(s):  
Cluster Model ◽  
Substrate Binding ◽  
Binding Mode ◽  
Femo Cofactor
Sign in / Sign up

Export Citation Format

Share Document