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Related Concept Videos

Inorganic Nitrogen Assimilation01:22

Inorganic Nitrogen Assimilation

Nitrogen is an essential element in biological systems, forming a crucial component of proteins, nucleic acids, and other cellular constituents. Many bacteria and archaea acquire nitrogen in the form of nitrate (NO₃⁻) or ammonia (NH₃), which are then assimilated into biomolecules through specific enzymatic pathways.Assimilatory Nitrate ReductionWhen nitrate enters the cell, it undergoes a two-step reduction process known as assimilatory nitrate reduction. Initially, the enzyme nitrate reductase...
Structure of Amines01:19

Structure of Amines

The hybridized nitrogen atom in amines possesses a lone pair of electrons and is bound to three substituents with a bond angle of around 108°, which is less than the tetrahedral angle of 109.5°. However, the C–N–H bond angle is slightly larger at 112°, with a carbon–nitrogen bond length of 147 pm. This carbon–nitrogen bond length of of amines is longer than the carbon–oxygen bond of alcohols (143 pm) but shorter than alkanes’ carbon–carbon bond (154 pm). These aspects are illustrated in Figure...
Overview of Nitrogen Metabolism01:20

Overview of Nitrogen Metabolism

Nitrogen is a very important element for life because it is a major constituent of proteins and nucleic acids. It is a macronutrient, and in nature, it is recycled from organic compounds and stored in the form of  ammonia, ammonium ions, nitrate, nitrite, or  nitrogen gas by many metabolic processes. Many of these metabolic processes are carried out only by prokaryotes.
The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen (N2) from the air, but this nitrogen...
2° Amines to N-Nitrosamines: Reaction with NaNO201:20

2° Amines to N-Nitrosamines: Reaction with NaNO2

Secondary amines react with nitrous acid to form N-nitrosamines, as depicted in Figure 1. Nitrous acid, a weak and unstable acid, is formed in situ from an aqueous solution of sodium nitrite and strong acids, such as hydrochloric acid or sulfuric acid, in cold conditions. In the presence of an acid, the nitrous acid gets protonated. The subsequent loss of water results in the formation of the electrophile known as nitrosonium ion.
Aldehydes and Ketones with Amines: Imine Formation Mechanism01:23

Aldehydes and Ketones with Amines: Imine Formation Mechanism

Imine formation involves the addition of carbonyl compounds to a primary amine. It begins with the generation of carbinolamine through a series of steps involving an initial nucleophilic attack and then several proton transfer reactions. The second part includes the elimination of water, as a leaving group, to give the imine.
Imines are formed under mildly acidic conditions. A pH of 4.5 is ideal for the reaction.
If the pH is low or the solution is too acidic, the reaction slows down in the...
Acid Halides to Amides: Aminolysis01:07

Acid Halides to Amides: Aminolysis

Aminolysis is a nucleophilic acyl substitution reaction, where ammonia or amines act as nucleophiles to give the substitution product. Acid halides react with ammonia, primary amines, and secondary amines to yield primary, secondary, and tertiary amides, respectively.
In the first step of the aminolysis mechanism, the amine attacks the carbonyl carbon of the acyl chloride to form a tetrahedral intermediate. In the second step, the carbonyl group is re-formed with the elimination of a chloride...

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Nitropeptide Profiling and Identification Illustrated by Angiotensin II
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Nitropeptide Profiling and Identification Illustrated by Angiotensin II

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The solution of nitrogen inversion in amidases.

Per-Olof Syrén1

  • 1Institute of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany. per-olof.syren@itb.uni-stuttgart.de

The FEBS Journal
|March 20, 2013
PubMed
Summary

Enzymes use two main strategies to overcome the challenge of amide bond hydrolysis: stabilizing transition states with hydrogen bonds or employing proton shuttle mechanisms. This research explores these catalytic solutions for enzyme and drug design.

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Measurement of the Potential Rates of Dissimilatory Nitrate Reduction to Ammonium Based on 14NH4+/15NH4+ Analyses via Sequential Conversion to N2O
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A General Method for Detecting Nitrosamide Formation in the In Vitro Metabolism of Nitrosamines by Cytochrome P450s
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A General Method for Detecting Nitrosamide Formation in the In Vitro Metabolism of Nitrosamines by Cytochrome P450s

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Measurement of the Potential Rates of Dissimilatory Nitrate Reduction to Ammonium Based on 14NH4+/15NH4+ Analyses via Sequential Conversion to N2O
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Published on: September 25, 2017

Area of Science:

  • Biochemistry
  • Enzymology
  • Structural Biology

Background:

  • Enzyme-catalyzed amide bond hydrolysis requires specific nitrogen lone pair orientation.
  • Stereoelectronic effects in tetrahedral intermediates necessitate nitrogen inversion or rotation.
  • Existing literature highlights challenges in achieving productive conformations for amide bond hydrolysis.

Purpose of the Study:

  • To review recent mechanistic findings on amide nitrogen lone pair conformation.
  • To demonstrate nature's evolved catalytic strategies for amide bond hydrolysis.
  • To explore the implications for enzyme and drug design.

Main Methods:

  • Literature review of mechanistic findings.
  • Molecular modeling to analyze hydrogen bond stabilization strategies.
  • Discussion of proton shuttle mechanisms.

Main Results:

  • Two primary catalytic strategies identified: hydrogen bond stabilization of inversion transition states and concerted proton shuttle mechanisms.
  • Molecular modeling confirms the generality of the hydrogen bond strategy across various amidases/proteases, including the proteasome.
  • Proton shuttle mechanisms offer an alternative route to avoid inversion.

Conclusions:

  • Enzymes employ distinct strategies to overcome stereoelectronic constraints in amide bond hydrolysis.
  • Understanding these mechanisms is crucial for advancing enzyme and drug design beyond traditional active site motifs.
  • Knowledge of general active site interactions is vital for efficient catalysis.