Inhibition of bacterial D-3-hydroxybutyrate dehydrogenase by substrates and substrate analogues

D-3-Hydroxybutyrate dehydrogenase (Pseudomonas lemoignei, EC 1.1.1.30) is subject to substrate inhibition by acetoacetate at concentrations above 5 mM but not by D-3-hydroxybutyrate at concentrations up to 50 mM. NADH causes substrate inhibition at concentrations over 0.1 mM as does NAD. Kinetic analysis suggests that substrate inhibition by acetoacetate is due to its binding to enzyme lacking NADH, a consequence of the ordered bibi mechanism. Substrate inhibition by NADH and NAD arises from binding of these species to a secondary site. This is confirmed by kinetics which indicate that ADP and ATP compete with NAD and NADH at both sites.New analogues of acetoacetate were synthesized to test the specificity requirements of the acetoacetate binding site which has been proposed to contain a hydrogen bond donor and a cation spaced to receive acetoacetate. Both dimethoxyphosphinylacetate and methyl 2-methoxyphosphinylacetate fulfill the structural requirements and are effective. They thus join methyl acetonylphosphonate as the only known competitive inhibitors for the acetoacetate site, confirming the proposed structure.

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Structure and activity of the tyrosy1-tRNA synthetase: the hydrogen bond in catalysis and specificity

Philosophical Transactions of the Royal Society of London. Series A, Mathematical and Physical Sciences ◽

10.1098/rsta.1986.0041 ◽

1986 ◽

Vol 317 (1540) ◽

pp. 305-320 ◽

Cited By ~ 16

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonding ◽

Transition State ◽

Binding Site ◽

Electrostatic Interactions ◽

Bacillus Stearothermophilus ◽

Trna Synthetase ◽

Binding Energies ◽

Hydrogen Bond Donor ◽

Differential Binding

The role ofhydrogen bonding in specificity, binding and catalysis by the tyrosyl-tRNA synthetase from Bacillus stearothermophilus has been investigated by systematic mutation of residues which form hydrogen bonds with substrates during the reaction between ATP and tyrosine to form tyrosyl adenylate. Data on hydrogen bonding as a determinant of biological specificity are summarized thus: deletion of an hydrogen-bond donor or acceptor between the enzyme and substrate to leave an unpaired but uncharged acceptor or donor weakens binding by only 2-7 kJ mol -1 ; but deletion to leave an unpaired but charged acceptor or donor weakens binding by some 17 kJ mol -1 or so. Hydrogen bonding is found to have a profound role in catalysis by mediating the differential binding of substrates, transition states and products. The formation of tyrosyl adenylate is not catalysed by classical mechanisms of acid-base or nucleophilic catalysis but the enhancement of rate is solely a result of a combination ofhydrogen bonding and electrostatic interactions which stabilize the transition state of the substrates relative to their ground states. The binding energy of ATP increases by more than 29 kJ mol -1 as it passes through the transition state, enhancing the rate by more than a factor of 10 5 . The residues involved in differential binding are spread over the molecule, away from the seat of reaction. The catalysis is delocalized over the whole binding site and not restricted to one or two specific residues. Some regions of the binding site are complementary in structure to the intermediate, tyrosyl adenylate. The apparent binding energies of certain side chains increase as the reaction proceeds, being weakest in the enzyme—substrate complex, stronger in the enzyme-transition-state complex and strongest in the enzyme-intermediate complex. This converts the unfavourable equilibrium constant for the formation of tyrosyl adenylate in solution to a favourable value for the enzyme-bound reagents and helps sequester the reactive tyrosyl adenylate.

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Diversifying molecular and topological space via a supramolecular solid-state synthesis: a purely organic mok net sustained by hydrogen bonds

IUCrJ ◽

10.1107/s2052252519011382 ◽

2019 ◽

Vol 6 (6) ◽

pp. 1032-1039 ◽

Cited By ~ 3

Author(s):

Shalisa M. Oburn ◽

Michael A. Sinnwell ◽

Devin P. Ericson ◽

Eric W. Reinheimer ◽

Davide M. Proserpio ◽

...

Keyword(s):

Hydrogen Bond ◽

Solid State ◽

Topological Space ◽

Organic Molecule ◽

Three Dimensional ◽

Protecting Group ◽

Hydrogen Bond Donor ◽

Hydrogen Bond Acceptor ◽

Structural Requirements ◽

Donor And Acceptor

A three-dimensional hydrogen-bonded network based on a rare mok topology has been constructed using an organic molecule synthesized in the solid state. The molecule is obtained using a supramolecular protecting-group strategy that is applied to a solid-state [2+2] photodimerization. The photodimerization affords a novel head-to-head cyclobutane product. The cyclobutane possesses tetrahedrally disposed cis-hydrogen-bond donor (phenolic) and cis-hydrogen-bond acceptor (pyridyl) groups. The product self-assembles in the solid state to form a mok network that exhibits twofold interpenetration. The cyclobutane adopts different conformations to provide combinations of hydrogen-bond donor and acceptor sites to conform to the structural requirements of the mok net.

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Synthesis and kinetic evaluation of 4-deoxymaltopentaose and 4-deoxymaltohexaose as inhibitors of muscle and potato α-glucan phosphorylases

Biochemical Journal ◽

10.1042/bj3380251 ◽

1999 ◽

Vol 338 (2) ◽

pp. 251-256 ◽

Cited By ~ 9

Author(s):

Renee MOSI ◽

Stephen G. WITHERS

Keyword(s):

Kinetic Analysis ◽

Binding Site ◽

Transfer Reaction ◽

Binding Mode ◽

Rabbit Muscle ◽

Kinetic Evaluation ◽

Substrate Analogues ◽

Muscle Phosphorylase ◽

Insight Into

α-Glucan phosphorylases degrade linear or branched oligosaccharides via a glycosyl transfer reaction, occurring with retention of configuration, to generate α-glucose-1-phosphate (G1P). We report here the chemoenzymic synthesis of two incompetent oligosaccharide substrate analogues, 4-deoxymaltohexaose (4DG6) and 4-deoxymaltopentaose (4DG5), for use in probing this mechanism. A kinetic analysis of the interactions of 4DG5 and 4DG6 with both muscle and potato phosphorylases was completed to provide insight into the nature of the binding mode of oligosaccharide to phosphorylase. The 4-deoxy-oligosaccharides bind competitively with maltopentaose and non-competitively with respect to orthophosphate or G1P in each case, indicating binding in the oligosaccharide binding site. Further, 4DG5 and 4DG6 were found to bind to potato and muscle phosphorylases some 10–40-fold tighter than does maltopentaose. Similar increases in affinity as a consequence of 4-deoxygenation were observed previously for the binding of polymeric glycogen analogues to rabbit muscle phosphorylase [Withers (1990) Carbohydr. Res. 196, 61–73].

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ROLE OF THE CONSERVATIVE INTERHELICAL HYDROGEN BOND SER74-TRP158 AT THE CHOLESTEROL BINDING SITE IN THE CONFORMATIONAL STABILITY OF THE b2-ADRENERGIC RECEPTOR: MOLECULAR DYNAMICS SIMULATION

Журнал структурной химии ◽

10.15372/jsc20170224 ◽

2017 ◽

Keyword(s):

Molecular Dynamics ◽

Hydrogen Bond ◽

Molecular Dynamics Simulation ◽

Binding Site ◽

Adrenergic Receptor ◽

Conformational Stability ◽

Dynamics Simulation ◽

Cholesterol Binding

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Faculty Opinions recommendation of Selective stabilization of the chorismate mutase transition state by a positively charged hydrogen bond donor.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1012843.187412 ◽

2003 ◽

Author(s):

Arieh Warshel

Keyword(s):

Hydrogen Bond ◽

Transition State ◽

Chorismate Mutase ◽

Hydrogen Bond Donor ◽

Selective Stabilization ◽

Positively Charged

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Faculty Opinions recommendation of Potent Inhibitors of Hepatitis C Virus NS3 Protease: Employment of a Difluoromethyl Group as a Hydrogen-Bond Donor.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.732705180.793543145 ◽

2018 ◽

Author(s):

Miles Congreve ◽

Mark Pickworth

Keyword(s):

Hydrogen Bond ◽

Hepatitis C Virus ◽

Hepatitis C ◽

Hydrogen Bond Donor ◽

Ns3 Protease

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Probing the ionization state of substrate α-d-glucopyranosyl phosphate bound to glycogen phosphorylase b

Biochemical Journal ◽

10.1042/bj3081017 ◽

1995 ◽

Vol 308 (3) ◽

pp. 1017-1023 ◽

Cited By ~ 1

Author(s):

I P Street ◽

S G Withers

Keyword(s):

Active Site ◽

Glycogen Phosphorylase ◽

Ph Dependence ◽

Substrate Inhibition ◽

19F Nmr ◽

Ionization State ◽

Nmr Studies ◽

Substrate Analogues ◽

Glycogen Phosphorylase B ◽

Pka Value

The ionization state of the substrate alpha-D-glucopyranosyl phosphate bound at the active site of glycogen phosphorylase has been probed by a number of techniques. Values of Ki determined for a series of substrate analogue inhibitors in which the phosphate moiety bears differing charges suggest that the enzyme will bind both the monoanionic and dianionic substrates with approximately equal affinity. These results are strongly supported by 31P- and 19F-NMR studies of the bound substrate analogues alpha-D-glucopyranosyl 1-methylenephosphonate and 2-deoxy-2-fluoro-alpha-D-glucopyranosyl phosphate, which also suggest that the substrate can be bound in either ionization state. The pH-dependences of the inhibition constants K1 for these two analogues, which have substantially different phosphate pK2 values (7.3 and 5.9 respectively), are found to be essentially identical with the pH-dependence of K(m) values for the substrate, inhibition decreasing according to an apparent pKa value of 7.2. This again indicates that there is no specificity for monoanion or dianion binding and also reveals that binding is associated with the uptake of a proton. As the bound substrate is not protonated, this proton must be taken up by the proton.

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Aliphatic Carboxylic Acid as Hydrogen-Bond Donor for Converting CO2 and Epoxide into Cyclic Carbonate under Mild Conditions

New Journal of Chemistry ◽

10.1039/d1nj01285a ◽

2021 ◽

Author(s):

Zheng Wang ◽

Yajun Wang ◽

Qianjie Xie ◽

Zhiying Fan ◽

Yehua Shen

Keyword(s):

Hydrogen Bond ◽

Carboxylic Acid ◽

Value Added ◽

Cyclic Carbonate ◽

Hydrogen Bond Donor ◽

Title Reaction ◽

Aliphatic Carboxylic Acid ◽

Mild Conditions ◽

Atmospheric Carbon

The coupling of CO2 and epoxide is promising way to reduce atmospheric carbon by converting it into value-added cyclic carbonate. Pursuing efficient catalysts is highly attractive for the title reaction....

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