Lysozyme

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Lysozyme
Identifiers
EC no. 3.2.1.17
CAS no. 9001-63-2
Databases
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BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO
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PMC articles
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NCBI proteins
Glycoside hydrolase, family 22, lysozyme
Lysozymecrystals1.png
Lysozyme crystals stained with methylene blue.
Identifiers
Symbol?
InterPro IPR000974

Lysozyme (EC 3.2.1.17, muramidase, N-acetylmuramide glycanhydrolase; systematic name peptidoglycan N-acetylmuramoylhydrolase) is an antimicrobial enzyme produced by animals that forms part of the innate immune system. It is a glycoside hydrolase that catalyzes the following process:

Contents

Hydrolysis of (1→4)-β-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrins

Peptidoglycan is the major component of gram-positive bacterial cell wall. [1] This hydrolysis in turn compromises the integrity of bacterial cell walls causing lysis of the bacteria.

Lysozyme is abundant in secretions including tears, saliva, human milk, and mucus. It is also present in cytoplasmic granules of the macrophages and the polymorphonuclear neutrophils (PMNs). Large amounts of lysozyme can be found in egg white. C-type lysozymes are closely related to α-lactalbumin in sequence and structure, making them part of the same glycoside hydrolase family 22. [2] In humans, the C-type lysozyme enzyme is encoded by the LYZ gene. [3] [4]

Hen egg white lysozyme is thermally stable, with a melting point reaching up to 72 °C at pH 5.0. [5] However, lysozyme in human milk loses activity very quickly at that temperature. [6] Hen egg white lysozyme maintains its activity in a large range of pH (6–9). [7] Its isoelectric point is 11.35. [8] The isoelectric point of human milk lysozyme is 10.5–11. [9]

Function and mechanism

The enzyme functions by hydrolyzing glycosidic bonds in peptidoglycans. The enzyme can also break glycosidic bonds in chitin, although not as effectively as true chitinases. [10]

Overview of the reaction catalysed by lysozyme Mecanism of action for Lysozyme.svg
Overview of the reaction catalysed by lysozyme

Lysozyme's active site binds the peptidoglycan molecule in the prominent cleft between its two domains. It attacks peptidoglycans (found in the cell walls of bacteria, especially Gram-positive bacteria), its natural substrate, between N-acetylmuramic acid (NAM) and the fourth carbon atom of N-acetylglucosamine (NAG).

Shorter saccharides like tetrasaccharide have also shown to be viable substrates but via an intermediate with a longer chain. [11] Chitin has also been shown to be a viable lysozyme substrate. Artificial substrates have also been developed and used in lysozyme. [12]

Mechanism

Phillips

The Phillips mechanism proposed that the enzyme's catalytic power came from both steric strain on the bound substrate and electrostatic stabilization of an oxo-carbenium intermediate. From X-ray crystallographic data, Phillips proposed the active site of the enzyme, where a hexasaccharide binds. The lysozyme distorts the fourth sugar (in the D or -1 subsite) in the hexasaccharide into a half-chair conformation. In this stressed state, the glycosidic bond is more easily broken. [13] An ionic intermediate containing an oxo-carbenium is created as a result of the glycosidic bond breaking. [14] Thus distortion causing the substrate molecule to adopt a strained conformation similar to that of the transition state will lower the energy barrier of the reaction. [15]

The proposed oxo-carbonium intermediate was speculated to be electrostatically stabilized by aspartate and glutamate residues in the active site by Arieh Warshel in 1978. The electrostatic stabilization argument was based on comparison to bulk water, the reorientation of water dipoles can cancel out the stabilizing energy of charge interaction. In Warshel's model, the enzyme acts as a super-solvent, which fixes the orientation of ion pairs and provides super-solvation (very good stabilization of ion pairs), and especially lower the energy when two ions are close to each other. [16]

The rate-determining step (RDS) in this mechanism is related to formation of the oxo-carbenium intermediate. There were some contradictory results to indicate the exact RDS. By tracing the formation of product (p-nitrophenol), it was discovered that the RDS can change over different temperatures, which was a reason for those contradictory results. At a higher temperature the RDS is formation of glycosyl enzyme intermediate and at a lower temperature the breakdown of that intermediate. [17]

Covalent intermediate of lysozyme enzyme, with covalent bond in black and experimental evidence as blue mesh. Lysozyme glycosyl covalent intermediate.gif
Covalent intermediate of lysozyme enzyme, with covalent bond in black and experimental evidence as blue mesh.

Covalent mechanism

Substrates in Vocadlo's experiment LysozymeIntermediates copy.png
Substrates in Vocadlo's experiment

In an early debate in 1969, Dahlquist proposed a covalent mechanism for lysozyme based on kinetic isotope effect, [14] but for a long time the ionic mechanism was more accepted. In 2001, a revised mechanism was proposed by Vocadlo via a covalent but not ionic intermediate. Evidence from ESI-MS analysis indicated a covalent intermediate. A 2-fluoro substituted substrate was used to lower the reaction rate and accumulate an intermediate for characterization. [19] The amino acid side-chains glutamic acid 35 (Glu35) and aspartate 52 (Asp52) have been found to be critical to the activity of this enzyme. Glu35 acts as a proton donor to the glycosidic bond, cleaving the C-O bond in the substrate, whereas Asp52 acts as a nucleophile to generate a glycosyl enzyme intermediate. The Glu35 reacts with water to form hydroxyl ion, a stronger nucleophile than water, which then attacks the glycosyl enzyme intermediate, to give the product of hydrolysis and leaving the enzyme unchanged. [20] This type of covalent mechanism for enzyme catalysis was first proposed by Koshland. [21]

More recently, quantum mechanics/ molecular mechanics (QM/MM) molecular dynamics simulations have been using the crystal of HEWL and predict the existence of a covalent intermediate. [22] Evidence for the ESI-MS and X-ray structures indicate the existence of covalent intermediate, but primarily rely on using a less active mutant or non-native substrate. Thus, QM/MM molecular dynamics provides the unique ability to directly investigate the mechanism of wild-type HEWL and native substrate. The calculations revealed that the covalent intermediate from the covalent mechanism is ~30 kcal/mol more stable than the ionic intermediate from the Phillips mechanism. [22] These calculations demonstrate that the ionic intermediate is extremely energetically unfavorable and the covalent intermediates observed from experiments using less active mutant or non-native substrates provide useful insight into the mechanism of wild-type HEWL.

Two Possible Mechanisms of Lysozyme JBSlysozymemechanism copy2.jpg
Two Possible Mechanisms of Lysozyme

Inhibition

Imidazole derivatives can form a charge-transfer complex with some residues (in or outside active center) to achieve a competitive inhibition of lysozyme. [23] In Gram-negative bacteria, the lipopolysaccharide acts as a non-competitive inhibitor by highly favored binding with lysozyme. [24]

Non-enzymatic action

Despite that the muramidase activity of lysozyme has been supposed to play the key role for its antibacterial properties, evidence of its non-enzymatic action was also reported. For example, blocking the catalytic activity of lysozyme by mutation of critical amino acid in the active site (52-Asp -> 52-Ser) does not eliminate its antimicrobial activity. [25] The lectin-like ability of lysozyme to recognize bacterial carbohydrate antigen without lytic activity was reported for tetrasaccharide related to lipopolysaccharide of Klebsiella pneumoniae . [26] Also, lysozyme interacts with antibodies and T-cell receptors. [27]

Enzyme conformation changes

Lysozyme exhibits two conformations: an open active state and a closed inactive state. The catalytic relevance was examined with single walled carbon nanotubes (SWCN) field effect transistors (FETs), where a singular lysozyme was bound to the SWCN FET. [28] Electronically monitoring the lysozyme showed two conformations, an open active site and a closed inactive site. In its active state lysozyme is able to processively hydrolyze its substrate, breaking on average 100 bonds at a rate of 15 per second. In order to bind a new substrate and move from the closed inactive state to the open active state requires two conformation step changes, while inactivation requires one step.

Superfamily

The conventional C-type lysozyme is part of a larger group of structurally and mechanistically related enzymes termed the lysozyme superfamily . This family unites GH22 C-type ("chicken") lysozymes with plant chitinase GH19, G-type ("goose") lysozyme GH23, V-type ("viral") lysozyme GH24 and the chitosanase GH46 families. The lysozyme-type nomenclature only reflects the source a type is originally isolated from and does not fully reflect the taxonomic distribution. [29] For example, humans and many other mammals have two G-type lysozyme genes, LYG1 and LYG2. [30]

Role in disease and therapy

LYZ
Available structures
PDB Ortholog search: PDBe RCSB
Identifiers
Aliases LYZ , LZM, LYZF1, lysozyme
External IDs OMIM: 153450 MGI: 96902 HomoloGene: 121490 GeneCards: LYZ
Orthologs
SpeciesHumanMouse
Entrez

4069

17110

Ensembl

ENSG00000090382

ENSMUSG00000069515

UniProt

P61626

P17897

RefSeq (mRNA)

NM_000239

NM_013590

RefSeq (protein)

NP_000230

NP_038618

Location (UCSC) Chr 12: 69.35 – 69.35 Mb Chr 10: 117.12 – 117.13 Mb
PubMed search [33] [34]
Wikidata
View/Edit Human View/Edit Mouse

Lysozyme is part of the innate immune system. Reduced lysozyme levels have been associated with bronchopulmonary dysplasia in newborns. [35] Piglets fed with human lysozyme milk can recover from diarrheal disease caused by E. coli faster. The concentration of lysozyme in human milk is 1,600 to 3,000 times greater than the concentration in livestock milk. Human lysozyme is more active than hen egg white lysozyme. A transgenic line of goats (with a founder named "Artemis") were developed to produce milk with human lysozyme to protect children from diarrhea if they can't get the benefits of human breastfeeding. [36] [37]

Since lysozyme is a natural form of protection from Gram-positive pathogens like Bacillus and Streptococcus , [38] it plays an important role in immunology of infants in human milk feeding. [39] Whereas the skin is a protective barrier due to its dryness and acidity, the conjunctiva (membrane covering the eye) is, instead, protected by secreted enzymes, mainly lysozyme and defensin. However, when these protective barriers fail, conjunctivitis results.

In certain cancers (especially myelomonocytic leukemia) excessive production of lysozyme by cancer cells can lead to toxic levels of lysozyme in the blood. High lysozyme blood levels can lead to kidney failure and low blood potassium, conditions that may improve or resolve with treatment of the primary malignancy.

Serum lysozyme is much less specific for diagnosis of sarcoidosis than serum angiotensin converting enzyme; however, since it is more sensitive, it is used as a marker of sarcoidosis disease activity and is suitable for disease monitoring in proven cases. [40]

Chemical synthesis

The first chemical synthesis of a lysozyme protein was attempted by Prof. George W. Kenner and his group at the University of Liverpool in England. [41] This was finally achieved in 2007 by Thomas Durek in Steve Kent's lab at the University of Chicago who made a synthetic functional lysozyme molecule. [42]

Other applications

Lysozyme crystals have been used to grow other functional materials for catalysis and biomedical applications. [43] [44] [45] Lysozyme is a commonly used enzyme for lysing gram positive bacteria. [46] Due to the unique function of lysozyme in which it can digest the cell wall and causes osmotic shock (burst the cell by suddenly changing solute concentration around the cell and thus the osmotic pressure), lysozyme is commonly used in lab setting to release proteins from bacterium periplasm while the inner membrane remains sealed as vesicles called the spheroplast. [47] [48]

For example, E. coli can be lysed using lysozyme to free the contents of the periplasmic space. It is especially useful in lab setting for trying to collect the contents of the periplasm. [1] Lysozyme treatment is optimal at particular temperatures, pH ranges, and salt concentrations. Lysozyme activity increases with increasing temperatures, up to 60 degrees Celsius, with a pH range of 6.0-7.0. The salts present also affect lysozyme treatment, where some assert inhibitory effects, and others promote lysis via lysozyme treatment. Sodium chloride induces lysis, but at high concentrations, it is an active inhibitor of lysis. Similar observations have been seen with the use of potassium salts. Slight variations are present due to differences in bacterial strains. [49] A consequence of the use of lysozyme in extracting recombinant proteins for protein crystallization is that the crystal may be contaminated with units of lysozyme, producing a physiologically irrelevant combination. In fact, some proteins simply cannot crystalize without such contamination. [50] [51]

Furthermore, lysozyme can serve as a tool in the expression of toxic recombinant proteins. Expressing recombinant proteins in BL21(DE3) strains is typically accomplished by the T7-RNA-polymerase. Via IPTG induction, the UV-5 repressor is inhibited, leading to the transcription of the T7-RNA-polymerase and thereby of the protein of interest. Nonetheless, a basal level of the T7-RNA-polymerase is observable even without induction. T7 lysozyme acts as an inhibitor of the T7-RNA-polymerase. Newly invented strains, containing a helper plasmid (pLysS), constitutively co-express low levels of T7 lysozyme, providing high stringency and consistent expression of the toxic recombinant protein. [52]

History

The antibacterial property of hen egg white, due to the lysozyme it contains, was first observed by Laschtschenko in 1909. [53] The bacteria-killing activity of nasal mucus was demonstrated in 1922 by Alexander Fleming, the discoverer of penicillin, who coined the term "lysozyme". [54] He is reported as saying: "As this substance has properties akin to those of ferments I have called it a 'Lysozyme'." [55] Fleming went on to show that an enzymic substance was present in a wide variety of secretions and was capable of rapidly lysing (i.e. dissolving) different bacteria, particularly a yellow "coccus" that he studied". [56]

Lysozyme was first crystallised by Edward Abraham in 1937, enabling the three-dimensional structure of hen egg white lysozyme to be described by David Chilton Phillips in 1965, when he obtained the first 2-ångström (200 pm) resolution model via X-ray crystallography. [57] [58] The structure was publicly presented at a Royal Institution lecture in 1965. [59] Lysozyme was the second protein structure and the first enzyme structure to be solved via X-ray diffraction methods, and the first enzyme to be fully sequenced that contains all twenty common amino acids. [60] As a result of Phillips' elucidation of the structure of lysozyme, it was also the first enzyme to have a detailed, specific mechanism suggested for its method of catalytic action. [61] [62] [63] This work led Phillips to provide an explanation for how enzymes speed up a chemical reaction in terms of its physical structures. The original mechanism proposed by Phillips was more recently revised. [19]

See also

Related Research Articles

<span class="mw-page-title-main">Enzyme</span> Large biological molecule that acts as a catalyst

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Peptidoglycan or murein is a unique large macromolecule, a polysaccharide, consisting of sugars and amino acids that forms a mesh-like peptidoglycan layer (sacculus) that surrounds the bacterial cytoplasmic membrane. The sugar component consists of alternating residues of β-(1,4) linked N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM). Attached to the N-acetylmuramic acid is an oligopeptide chain made of three to five amino acids. The peptide chain can be cross-linked to the peptide chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a structural role in the bacterial cell wall, giving structural strength, as well as counteracting the osmotic pressure of the cytoplasm. This repetitive linking results in a dense peptidoglycan layer which is critical for maintaining cell form and withstanding high osmotic pressures, and it is regularly replaced by peptidoglycan production. Peptidoglycan hydrolysis and synthesis are two processes that must occur in order for cells to grow and multiply, a technique carried out in three stages: clipping of current material, insertion of new material, and re-crosslinking of existing material to new material.

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<span class="mw-page-title-main">Pseudopeptidoglycan</span>

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<span class="mw-page-title-main">Glycoside hydrolase</span> Class of enzymes which break glycosidic bonds via hydrolysis

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<span class="mw-page-title-main">Glycoside hydrolase family 24</span>

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<span class="mw-page-title-main">Glucanase</span>

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References

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  2. ↑ Williams S, Vocadlo D. "Glycoside hydrolase family 22". Cazypedia. Retrieved 11 April 2017.
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  7. ↑ "Lysozyme, Product information" (PDF). Sigma-Aldrich.
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  10. ↑ Skujiņś J, Puķite A, McLaren AD (December 1973). "Adsorption and reactions of chitinase and lysozyme on chitin". Molecular and Cellular Biochemistry. 2 (2): 221–228. doi:10.1007/BF01795475. PMID   4359167. S2CID   27906558.
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  12. ↑ Höltje JV (1 January 1996). "Lysozyme Substrates". Lysozymes: Model Enzymes in Biochemistry and Biology. Experientia Supplementum. Vol. 75. pp. 105–110. doi:10.1007/978-3-0348-9225-4_7 (inactive 4 April 2024). ISBN   978-3-0348-9952-9. PMID   8765297.{{cite book}}: CS1 maint: DOI inactive as of April 2024 (link)
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  14. 1 2 Dahlquist FW, Rand-Meir T, Raftery MA (October 1969). "Application of secondary α-deuterium kinetic isotope effects to studies of enzyme catalysis. Glycoside hydrolysis by lysozyme and β-glucosidase". Biochemistry. 8 (10): 4214–4221. doi:10.1021/bi00838a045. PMID   5388150.
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  17. ↑ Weber JP, Fink AL (October 1980). "Temperature-dependent change in the rate-limiting step of β-glucosidase catalysis". The Journal of Biological Chemistry. 255 (19): 9030–9032. doi: 10.1016/S0021-9258(19)70521-3 . PMID   6773958.
  18. ↑ "Hen Egg-White (HEW) Lysozyme - Proteopedia, life in 3D".
  19. 1 2 Vocadlo DJ, Davies GJ, Laine R, Withers SG (August 2001). "Catalysis by hen egg-white lysozyme proceeds via a covalent intermediate" (PDF). Nature. 412 (6849): 835–838. Bibcode:2001Natur.412..835V. doi:10.1038/35090602. PMID   11518970. S2CID   205020153.
  20. ↑ Grisham CM, Garrett RH (2007). "Chapter 14: Mechanism of enzyme action". Biochemistry. Australia: Thomson Brooks/Cole. pp. 467–9. ISBN   978-0-495-11912-8.
  21. ↑ Koshland DE (November 1953). "Stereochemistry and the Mechanism of Enzymatic Reactions". Biological Reviews. 28 (4): 416–436. doi:10.1111/j.1469-185X.1953.tb01386.x. S2CID   86709302.
  22. 1 2 Bowman AL, Grant IM, Mulholland AJ (October 2008). "QM/MM simulations predict a covalent intermediate in the hen egg white lysozyme reaction with its natural substrate". Chemical Communications (37): 4425–4427. doi:10.1039/b810099c. PMID   18802578.
  23. ↑ Swan ID (March 1972). "The inhibition of hen egg-white lysozyme by imidazole and indole derivatives". Journal of Molecular Biology. 65 (1): 59–62. doi:10.1016/0022-2836(72)90491-3. PMID   5063023.
  24. ↑ Ohno N, Morrison DC (March 1989). "Lipopolysaccharide interaction with lysozyme. Binding of lipopolysaccharide to lysozyme and inhibition of lysozyme enzymatic activity". The Journal of Biological Chemistry. 264 (8): 4434–4441. doi: 10.1016/S0021-9258(18)83761-9 . PMID   2647736.
  25. ↑ Ibrahim HR, Matsuzaki T, Aoki T (September 2001). "Genetic evidence that antibacterial activity of lysozyme is independent of its catalytic function". FEBS Letters. 506 (1): 27–32. doi: 10.1016/S0014-5793(01)02872-1 . PMID   11591365. S2CID   21593262.
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