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Related Concept Videos

Urea Cycle01:23

Urea Cycle

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The urea cycle describes how liver cells convert ammonia to urea. Ammonia is a toxic waste product of protein catabolism. Land animals must convert ammonia into the less toxic urea which can be safely eliminated by the kidneys through urine. Marine animals excrete ammonia directly, and the surrounding water dilutes the ammonia to safe levels.
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Aldehydes and Ketones with Amines: Enamine Formation Mechanism01:14

Aldehydes and Ketones with Amines: Enamine Formation Mechanism

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Enamine formation involves the addition of carbonyl compounds to a secondary amine through a series of reactions. The mechanism begins with the generation of carbinolamine, a nucleophilic attack followed by several proton transfer reactions. The hydroxyl group of the carbinolamine is converted into water to make a better leaving group that can push the reaction forward by eliminating a water molecule. In enamine formation, the last step involves the abstraction of a proton from the α carbon to...
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Aldehydes and Ketones with Amines: Imine Formation Mechanism01:23

Aldehydes and Ketones with Amines: Imine Formation Mechanism

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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...
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Aldehydes and Ketones with Amines: Imine and Enamine Formation Overview01:16

Aldehydes and Ketones with Amines: Imine and Enamine Formation Overview

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Primary amines react with carbonyl compounds—aldehydes and ketones—to generate imines. Imines consist of a C=N double bond and are named Schiff bases after its discoverer—the German chemist Hugo Schiff. On the other hand, secondary amines react with carbonyl compounds to give enamines. In enamines, the presence of a C=C double bond adjacent to the nitrogen atom leads to the delocalization of the lone pair.
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Amides to Carboxylic Acids: Hydrolysis01:28

Amides to Carboxylic Acids: Hydrolysis

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Amides can undergo either acid-catalyzed hydrolysis or base-promoted hydrolysis through a typical nucleophilic acyl substitution. Each hydrolysis requires severe conditions.
Acid-catalyzed hydrolysis:
Hydrolysis of amides under acidic conditions yields carboxylic acids. Since the reaction occurs slowly, hydrolysis requires the conditions of heat.
The mechanism begins with the protonation of the carbonyl oxygen by the acid catalyst. The protonation makes the amide carbonyl carbon more...
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Acid Halides to Amides: Aminolysis01:07

Acid Halides to Amides: Aminolysis

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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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Hot Biological Catalysis: Isothermal Titration Calorimetry to Characterize Enzymatic Reactions
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Structure and function of urea amidolyase.

Jing Zhao1, Li Zhu2, Chen Fan1

  • 1Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Bioscience Reports
|December 22, 2017
PubMed
Summary

This study reveals the structure of Kluyveromyces lactis urea amidolyase (KlUA), a key enzyme in nitrogen recycling. The KlUA holo-enzyme is essential for optimal activity, unlike separate urea carboxylase and allophanate hydrolase domains.

Keywords:
biotincrystallographyhydrolasesnitrogen metabolismurea amidolyase

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Microbiology

Background:

  • Urea amidolyase (UA) is crucial for microorganisms to utilize urea as a nitrogen source, converting it to ammonium.
  • UA is vital for nitrogen recycling in the biosphere and comprises urea carboxylase (UC) and allophanate hydrolase (AH) domains.
  • In some species, UC and AH are encoded by separate genes.

Purpose of the Study:

  • To elucidate the structure of Kluyveromyces lactis urea amidolyase (KlUA).
  • To understand the mechanism of reaction intermediate translocation within KlUA.
  • To investigate the role of holo-enzyme formation in KlUA activity.

Main Methods:

  • X-ray crystallography was used to determine the structure of KlUA.
  • Biochemical experiments were conducted to probe the enzyme's mechanism.
  • Comparative analysis with studies on UA from other organisms was performed.

Main Results:

  • The crystal structure of KlUA revealed a compact homo-dimer (400 kDa).
  • Mechanism of reaction intermediate translocation was elucidated through structure-inspired experiments.
  • Holo-enzyme formation was found to be essential for optimal KlUA activity.
  • Evidence suggests that separately encoded UC and AH domains may not form an active complex as efficiently as the KlUA holo-enzyme.

Conclusions:

  • The KlUA structure provides insights into the enzyme's mechanism and quaternary structure.
  • Holo-enzyme formation is critical for the efficient function of urea amidolyase.
  • Separate UC and AH genes may lead to less efficient urea-to-ammonium conversion compared to a single holo-enzyme complex.