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Related Concept Videos

Induced-fit Model01:13

Induced-fit Model

Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...
Predicting Products: SN1 vs. SN202:27

Predicting Products: SN1 vs. SN2

Nucleophilic substitution reactions of alkyl halides can proceed via an SN1 or an SN2 mechanism. While in SN2 reactions, the nucleophile attacks the substrate simultaneously as the leaving group departs, in SN1 reactions, the substrate first dissociates to give the carbocation intermediate. Various factors such as the structure of the substrate, the strength of the nucleophile, and the nature of the solvent promote one mechanism over the other.
With increased substitution on the alkyl halide,...
Enzymes02:34

Enzymes

Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Leaving Groups02:14

Leaving Groups

The nature of leaving groups strongly influences the outcome of a nucleophilic substitution reaction.
In general, in a nucleophilic substitution reaction, a nucleophile displaces a functional group, called the leaving group, from the substrate to give a substituted product. A leaving group departs the substrate molecule through heterolytic cleavage, taking the pair of electrons with it to become a relatively stable weak base in the form of an anion or a neutral molecule.  
In a nucleophilic...
SN2 Reaction: Stereochemistry02:23

SN2 Reaction: Stereochemistry

In an SN2 reaction, the nucleophilic attack on the substrate and departure of the leaving group occurs simultaneously through a transition state. As the nucleophile approaches the substrate from the back-side, the configuration of the substrate carbon changes from tetrahedral to trigonal bipyramidal and then back to tetrahedral, leading to an inversion in the configuration of the product.
If the substrate is an achiral molecule at the α-carbon, the inversion of configuration is not observed.
Nucleophilic Substitution Reactions02:34

Nucleophilic Substitution Reactions

Historical perspective
In 1896, the German chemist Paul Walden discovered that he could interconvert pure enantiomeric (+) and (-) malic acids through a series of reactions. This conversion suggested the involvement of optical inversion during the substitution reaction. Further, in 1930, Sir Christopher Ingold described for the first time two different forms of nucleophilic substitution reactions, which are known as SN1 (nucleophilic substitution unimolecular) and SN2 (nucleophilic substitution...

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Related Experiment Video

Updated: Jul 6, 2026

Defining Substrate Specificities for Lipase and Phospholipase Candidates
08:59

Defining Substrate Specificities for Lipase and Phospholipase Candidates

Published on: November 23, 2016

Structural basis for substrate specificity in group I nucleoside hydrolases.

Elena Iovane1, Barbara Giabbai, Laura Muzzolini

  • 1Biocrystallography Unit, DIBIT San Raffaele Scientific Institute, via Olgettina 58, 20132 Milan, Italy.

Biochemistry
|March 26, 2008
PubMed
Summary
This summary is machine-generated.

This study reveals how specific mutations in nucleoside hydrolase (NH) enzymes alter substrate specificity. Researchers identified distinct amino acid roles in the hydrolysis of purine versus pyrimidine nucleosides.

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NMR-Based Activity Assays for Determining Compound Inhibition, IC50 Values, Artifactual Activity, and Whole-Cell Activity of Nucleoside Ribohydrolases
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Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods
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Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods

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NMR-Based Activity Assays for Determining Compound Inhibition, IC50 Values, Artifactual Activity, and Whole-Cell Activity of Nucleoside Ribohydrolases
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NMR-Based Activity Assays for Determining Compound Inhibition, IC50 Values, Artifactual Activity, and Whole-Cell Activity of Nucleoside Ribohydrolases

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Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods
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Analysis of Group IV Viral SSHHPS Using In Vitro and In Silico Methods

Published on: December 21, 2019

Area of Science:

  • Biochemistry
  • Enzymology
  • Structural Biology

Background:

  • Group I nucleoside hydrolases (NHs) exhibit varied substrate specificities, either targeting pyrimidines or hydrolyzing all nucleosides.
  • The underlying biochemical and structural reasons for these specificity differences remain largely unexplored.

Purpose of the Study:

  • To elucidate the binding interactions between the pyrimidine-specific NH YeiK from Escherichia coli and its slowly hydrolyzed substrate, inosine.
  • To investigate the structural basis for substrate specificity in group I NHs.

Main Methods:

  • Cryotrapping and X-ray crystallography were employed to characterize enzyme-substrate interactions.
  • Site-directed mutagenesis was used to probe the roles of specific amino acid residues in catalysis.

Main Results:

  • Structural analysis of the Michaelis complex informed the design of mutations.
  • Two point mutations in YeiK significantly enhanced catalytic efficiency towards purine nucleosides.
  • The integrity of a catalytic triad (two hydroxylated amino acids and histidine) is crucial for efficient inosine hydrolysis.
  • Mutations affecting the catalytic triad did not impact the hydrolysis of uridine, YeiK's preferred substrate.

Conclusions:

  • Distinct amino acid residues are involved in the hydrolysis of purine and pyrimidine nucleosides by group I NHs.
  • This provides the first direct evidence for differential substrate recognition mechanisms within this enzyme class.