scholarly journals Substrate inhibition by the blockage of product release and its control by tunnel engineering

2021 ◽  
Author(s):  
Piia Kokkonen ◽  
Andy Beier ◽  
Stanislav Mazurenko ◽  
Jiri Damborsky ◽  
David Bednar ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Substrate Inhibition ◽  
Tunnel Engineering ◽  
Product Release ◽  
Enzyme Product

Substrate inhibition can be caused by substrate binding to the enzyme–product complex and can be controlled rationally by targeting enzyme access tunnels.

scholarly journals Product inhibition studies on bovine liver carbamoyl phosphate synthetase

1974 ◽  
Vol 141 (3) ◽  
pp. 817-824 ◽  
Author(s):  
Keith R. F. Elliott ◽  
Keith F. Tipton
Keyword(s):  
Inorganic Phosphate ◽  
Substrate Binding ◽  
Inorganic Ions ◽  
Bovine Liver ◽  
Product Inhibition ◽  
Carbamoyl Phosphate Synthetase ◽  
Carbamoyl Phosphate ◽  
Product Release ◽  
Proposed Model ◽  
Inhibition Studies

A study of the product-inhibition patterns of carbamoyl phosphate synthetase from bovine liver is reported. Inhibition by adenosine, AMP and inorganic ions is also reported. The results are in agreement with the previously proposed model in which the order of substrate binding is ATPMg, followed by HCO3−, ATPMg and NH4+. The order of product release on the basis of the reported results is carbamoyl phosphate, followed by ADPMg, ADPMg and inorganic phosphate.

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.

scholarly journals Structure-Based Mutational Studies of Substrate Inhibition of Betaine Aldehyde Dehydrogenase BetB from Staphylococcus aureus

2014 ◽  
Vol 80 (13) ◽  
pp. 3992-4002 ◽  
Author(s):  
Chao Chen ◽  
Jeong Chan Joo ◽  
Greg Brown ◽  
Ekaterina Stolnikova ◽  
Andrei S. Halavaty ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Aldehyde Dehydrogenase ◽  
Active Sites ◽  
Mutational Analysis ◽  
Substrate Binding ◽  
Substrate Inhibition ◽  
Betaine Aldehyde Dehydrogenase ◽  
Uncharacterized Protein ◽  
Content Type ◽  
Betaine Aldehyde

ABSTRACTInhibition of enzyme activity by high concentrations of substrate and/or cofactor is a general phenomenon demonstrated in many enzymes, including aldehyde dehydrogenases. Here we show that the uncharacterized protein BetB (SA2613) fromStaphylococcus aureusis a highly specific betaine aldehyde dehydrogenase, which exhibits substrate inhibition at concentrations of betaine aldehyde as low as 0.15 mM. In contrast, the aldehyde dehydrogenase YdcW fromEscherichia coli, which is also active against betaine aldehyde, shows no inhibition by this substrate. Using the crystal structures of BetB and YdcW, we performed a structure-based mutational analysis of BetB and introduced the YdcW residues into the BetB active site. From a total of 32 mutations, those in five residues located in the substrate binding pocket (Val288, Ser290, His448, Tyr450, and Trp456) greatly reduced the substrate inhibition of BetB, whereas the double mutant protein H448F/Y450L demonstrated a complete loss of substrate inhibition. Substrate inhibition was also reduced by mutations of the semiconserved Gly234 (to Ser, Thr, or Ala) located in the BetB NAD+binding site, suggesting some cooperativity between the cofactor and substrate binding sites. Substrate docking analysis of the BetB and YdcW active sites revealed that the wild-type BetB can bind betaine aldehyde in both productive and nonproductive conformations, whereas only the productive binding mode can be modeled in the active sites of YdcW and the BetB mutant proteins with reduced substrate inhibition. Thus, our results suggest that the molecular mechanism of substrate inhibition of BetB is associated with the nonproductive binding of betaine aldehyde.

Substrate Binding, Catalysis, and Product Release

2004 ◽  
pp. 123-126
Author(s):  
W. Wallace Cleland
Keyword(s):  
Substrate Binding ◽  
Product Release

The molecular mechanism of the open–closed protein conformational cycle transitions and coupled substrate binding, activation and product release events in lysine 5,6-aminomutase

2016 ◽  
Vol 52 (38) ◽  
pp. 6399-6402 ◽  
Author(s):  
Hsin-Hsi Lo ◽  
Hsin-Hua Lin ◽  
Amarendra Nath Maity ◽  
Shyue-Chu Ke
Keyword(s):  
Molecular Mechanism ◽  
Bond Cleavage ◽  
Substrate Binding ◽  
Closed Cycle ◽  
Product Release

The contributions of Lys370α and Asp298α to the critical Co–C bond cleavage trigger and open–closed cycle transitions of lysine 5,6-aminomutase.

scholarly journals Conformational change in substrate binding, catalysis and product release: an open and shut case?

FEBS Letters ◽  
2004 ◽  
Vol 567 (1) ◽  
pp. 67-73 ◽  
Author(s):  
Alex Gutteridge ◽  
Janet Thornton
Keyword(s):  
Conformational Change ◽  
Substrate Binding ◽  
Product Release

The interplay of processivity, substrate inhibition and a secondary substrate binding site of an insect exo-β-1,3-glucanase

2007 ◽  
Vol 1774 (9) ◽  
pp. 1079-1091 ◽  
Author(s):  
Fernando A. Genta ◽  
Alexandra F. Dumont ◽  
Sandro R. Marana ◽  
Walter R. Terra ◽  
Clélia Ferreira
Keyword(s):  
Binding Site ◽  
Substrate Binding ◽  
Substrate Inhibition ◽  
Substrate Binding Site

Substrate Binding, Catalysis, and Product Release

2013 ◽  
pp. 347-349
Author(s):  
W.W. Cleland
Keyword(s):  
Substrate Binding ◽  
Product Release
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