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Overview for MACiE Entry M0203

Version history

General Information

EC Number: 3.2.1.17 (A member of the Hydrolases, Glycosylases, Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds)

Enzyme Name: lysozyme

Biological Species: Gallus gallus (Chicken)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 1dpx - STRUCTURE OF HEN EGG-WHITE LYSOZYME (Resolution = 1.65 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of Peptidoglycan (1,4-beta-linkage between N-acetylmuramic acid and N-acetyl-D-glucosamine)

Image of Water

right arrow

Image of N-Acetylmuramic acid

Image of Peptidoglycan (N-acetyl-D-glucosamine)

Peptidoglycan (1,4-beta-linkage between N-acetylmuramic acid and N-acetyl-D-glucosamine)
X00117
Water
C00001
CHEBI:15377
N-Acetylmuramic acid
C02713
CHEBI:47965
Peptidoglycan (N-acetyl-D-glucosamine)
C04394

Overall Comment: Enzyme catalyses the hydrolysis of 1 4-beta-linkages between N-acetylmuramic acid (NAM) and N-acetyl-D-glucosamine (NAG) residues in a peptidoglycan. There has been much debate about the mechanism of this enzyme with two major proposals having been put forward. The first is the so-called Phillips mechanism in which the enzyme proceeds via a oxycarbenium intermediate. The mechanism shown in MACiE is the one in which the enzyme proceeds via a covalent intermediate. This mechanism is supported through crystal structures, kinetic isotope experiments, stereochemical observations, computational studies and mutagenesis.


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Stepwise Description of the Reaction

Step 1Asp52 attacks the C1 of the peptidoglycan in a nucleophilic substitution that results in the NAG portion of the peptidoglycan being covalently attached to the enzyme and the NAM being released. NAM deprotonates Glu35.
Step 2Glu35 deprotonates water, which attacks the C1 of the covalently bound NAG intermediate in a nucleophilic substitution that results in the NAG product and free Asp52.

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Catalytic Residues Involved

Type Number Chain Location of Function
Asp 52 A Side Chain
Glu 35 A Side Chain

References

  1. D. J. Vocadlo et al. (2001), Nature, 412, 835-838. Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate.
    Medline: 11518970
  2. A. J. Kirby (2001), Nat. Struct. Biol., 8, 737-739. The lysozyme mechanism sorted - after 50 years.
    Medline: 11524668
  3. A. Bottoni et al. (2005), Proteins, 59, 118-130. A theoretical DFT investigation of the lysozyme mechanism: computational evidence for a covalent intermediate pathway.
    Medline: 15688446

Homologue information for M0203 (1dpx)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

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