Serine protease

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Serine protease
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Crystal structure of Trypsin, a typical serine protease.

Serine proteases (or serine endopeptidases) are

nucleophilic amino acid at the (enzyme's) active site.[1]
They are found ubiquitously in both
prokaryotes. Serine proteases fall into two broad categories based on their structure: chymotrypsin-like (trypsin-like) or subtilisin-like.[2]

Classification

The

PA clan
(superfamily) of proteases.

For superfamilies, P: superfamily, containing a mixture of nucleophile class families, S: purely serine proteases. superfamily. Within each superfamily, families are designated by their catalytic nucleophile, (S: serine proteases).

Hinge motion in disordered activation domain in Trypsinogen (PDB ID: 2PTN). The hinges predicted using PACKMAN Hinge prediction[3] are colored in blue (residues 23:28) and red (residues 175:182). The green colored region is the active site. Motion is generated using hdANM[4].
Families of serine proteases
Super-
family
Families Examples
SB S8, S53 Subtilisin (Bacillus licheniformis)
SC S9, S10, S15, S28, S33, S37
Sus scrofa
)
SE S11, S12, S13 D-Ala-D-Ala peptidase C (Escherichia coli)
SF S24, S26 Signal peptidase I (Escherichia coli)
SH S21, S73, S77, S78, S80 Cytomegalovirus
herpesvirus
5)
SJ S16, S50, S69
Lon-A peptidase (Escherichia coli
)
SK S14, S41, S49 Clp protease (Escherichia coli)
SO S74 Phage K1F endosialidase CIMCD self-cleaving protein (Enterobacteria phage K1F)
SP S59
Homo sapiens
)
SR S60
Homo sapiens
)
SS S66 Murein tetrapeptidase LD-carboxypeptidase (Pseudomonas aeruginosa)
ST S54 Rhomboid-1 (Drosophila melanogaster)
PA
S1, S3, S6, S7, S29, S30, S31, S32,
S39, S46, S55, S64, S65, S75
Bos taurus
)
PB S45, S63
Penicillin G acylase precursor (Escherichia coli
)
PC S51 Dipeptidase E (Escherichia coli)
PE P1 DmpA aminopeptidase (Brucella anthropi)
None S48, S62, S68, S71, S72, S79, S81

Substrate specificity

Serine proteases are characterised by a distinctive structure, consisting of two beta-barrel domains that converge at the catalytic active site. These enzymes can be further categorised based on their substrate specificity as either trypsin-like, chymotrypsin-like or elastase-like.[5]

Trypsin-like

Trypsin-like proteases cleave peptide bonds following a positively charged amino acid (lysine or arginine).[6] This specificity is driven by the residue which lies at the base of the enzyme's S1 pocket (generally a negatively charged aspartic acid or glutamic acid).

Chymotrypsin-like

The S1 pocket of chymotrypsin-like enzymes is more hydrophobic than in trypsin-like proteases. This results in a specificity for medium to large sized hydrophobic residues, such as tyrosine, phenylalanine and tryptophan.

Thrombin-like

These include thrombin, tissue activating plasminogen and plasmin. They have been found to have roles in coagulation and digestion as well as in the pathophysiology of neurodegenerative disorders such as Alzheimer's and Parkinson's induced dementia. Many highly-toxic thrombin-like serine protease isoforms are found in snake venoms.[7]

Elastase-like

Elastase-like proteases have a much smaller S1 cleft than either trypsin- or chymotrypsin-like proteases. Consequently, residues such as alanine, glycine and valine tend to be preferred.

Subtilisin-like

prokaryotes. Subtilisin is evolutionarily unrelated to the chymotrypsin-clan, but shares the same catalytic mechanism utilising a catalytic triad, to create a nucleophilic serine. This is the classic example used to illustrate convergent evolution, since the same mechanism evolved twice independently during evolution
.

Catalytic mechanism

serine protease reaction mechanism
serine protease reaction mechanism

The main player in the catalytic mechanism in the serine proteases is the catalytic triad. The triad is located in the active site of the enzyme, where catalysis occurs, and is preserved in all

amino acids: His 57, Ser 195 (hence the name "serine protease") and Asp 102. These three key amino acids each play an essential role in the cleaving ability of the proteases. While the amino acid members of the triad are located far from one another on the sequence of the protein, due to folding, they will be very close to one another in the heart of the enzyme. The particular geometry of the triad members are highly characteristic to their specific function: it was shown that the position of just four points of the triad characterize the function of the containing enzyme.[8]

In the event of catalysis, an ordered mechanism occurs in which several intermediates are generated. The catalysis of the peptide cleavage can be seen as a

substrate
binds (in this case, the polypeptide being cleaved), a product is released (the N-terminus "half" of the peptide), another substrate binds (in this case, water), and another product is released (the C-terminus "half" of the peptide).

Each amino acid in the triad performs a specific task in this process:

The whole reaction can be summarized as follows:

Additional stabilizing effects

It was discovered that additional amino acids of the protease, Gly 193 and Ser 195, are involved in creating what is called an oxyanion hole. Both Gly 193 and Ser 195 can donate backbone hydrogens for hydrogen bonding. When the

carbonyl double bond, fits perfectly into the oxyanion hole. In effect, serine proteases preferentially bind the transition state and the overall structure is favored, lowering the activation energy
of the reaction. This "preferential binding" is responsible for much of the catalytic efficiency of the enzyme.

Regulation of serine protease activity

Host organisms must ensure that the activity of serine proteases is adequately regulated. This is achieved by a requirement for initial protease activation, and the secretion of inhibitors.

Zymogen activation

postmortem investigations
, as the pancreas often digests itself before it can be assessed visually.

Zymogens are large, inactive structures, which have the ability to break apart or change into the smaller activated enzymes. The difference between zymogens and the activated enzymes lies in the fact that the active site for catalysis of the zymogens is distorted. As a result, the substrate polypeptide cannot bind effectively, and proteolysis does not occur. Only after activation, during which the conformation and structure of the zymogen change and the active site is opened, can proteolysis occur.

Zymogen Enzyme Notes
Trypsinogen trypsin When trypsinogen enters the
autocatalytic
.
Chymotrypsinogen chymotrypsin After the Arg 15 - Ile 16 bond in the chymotrypsinogen zymogen is cleaved by trypsin, the newly generated structure called a pi-chymotrypsin undergoes autolysis (self digestion), yielding active chymotrypsin.
Proelastase elastase It is activated by cleavage through trypsin.

As can be seen, trypsinogen activation to trypsin is essential, because it activates its own reaction, as well as the reaction of both chymotrypsin and elastase. Therefore, it is essential that this activation does not occur prematurely. There are several protective measures taken by the organism to prevent self-digestion:

  • The activation of trypsinogen by trypsin is relatively slow
  • The zymogens are stored in zymogen granules, capsules that have walls that are thought to be resistant to proteolysis.

Inhibition

There are certain inhibitors that resemble the tetrahedral intermediate, and thus fill up the active site, preventing the enzyme from working properly. Trypsin, a powerful digestive enzyme, is generated in the pancreas. Inhibitors prevent self-digestion of the pancreas itself.

Serine proteases are paired with serine protease inhibitors, which turn off their activity when they are no longer needed.[9][self-published source?]

Serine proteases are inhibited by a diverse group of

A1AT
, respectively. Artificial irreversible small molecule inhibitors include AEBSF and PMSF.

A family of arthropod serine peptidase inhibitors, called pacifastin, has been identified in locusts and crayfish, and may function in the arthropod immune system.[10]

Role in disease

Mutations may lead to decreased or increased activity of enzymes. This may have different consequences, depending on the normal function of the serine protease. For example, mutations in

SARS-CoV-2 fusion). Exogenous snake venom serine proteases cause a vast array of coagulopathies when injected in a host due to the lack of regulation of their activity.[7]

Diagnostic use

Determination of serine protease levels may be useful in the context of particular diseases.

Antimicrobial effect

Due to their catalytic activity, some serine proteases possess potent antimicrobial properties. Several in vitro studies have demonstrated the efficacy of some proteases in reducing virulence by cleaving viral surface proteins. Viral entry into host cells is mediated by the interaction of these surface proteins with the host cell. When these proteins are fragmented or inactivated on the viral surface, the viral entry is impaired, leading to a reduction in infectivity of a broad spectrum of pathologically relevant microorganisms like

hRSV and others.[11][12]

See also

References

  1. ^ Hedstrom L (December 2002). "Serine protease mechanism and specificity". Chemical Reviews. 102 (12): 4501–4524.
    PMID 12475199
    .
  2. ^ Madala PK, Tyndall JD, Nall T, Fairlie DP (June 2010). "Update 1 of: Proteases universally recognize beta strands in their active sites". Chemical Reviews. 110 (6): PR1–P31.
    PMID 20377171
    .
  3. .
  4. .
  5. ^ Ovaere P, Lippens S, Vandenabeele P, Declercq W (September 2009). "The emerging roles of serine protease cascades in the epidermis". Trends in Biochemical Sciences. 34 (9): 453–463.
    PMID 19726197
    .
  6. ^ Evnin LB, Vásquez JR, Craik CS (September 1990). "Substrate specificity of trypsin investigated by using a genetic selection". Proceedings of the National Academy of Sciences of the United States of America. 87 (17): 6659–6663.
    PMID 2204062
    .
  7. ^ .
  8. ^ Iván G, Szabadka Z, Ordög R, Grolmusz V, Náray-Szabó G (June 2009). "Four spatial points that define enzyme families". Biochemical and Biophysical Research Communications. 383 (4): 417–420.
    PMID 19364497
    .
  9. ^ "Kimball's Biology Pages, Serine Proteases". Archived from the original on 2005-12-13. Retrieved 2008-06-02.
  10. S2CID 8797134
    .
  11. .
  12. .

External links