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SECTION B
PEPTIDASES
SECTION B
PEPTIDASES
CHAPTER 10
AN INTRODUCTION TO PEPTIDASES AND THE MEROPS
DATABASE
NEIL D. RAWLINGS
∗
, FRASER R. MORTON AND ALAN J. BARRETT
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
∗
ndr@sanger.ac.uk
1. INTRODUCTION
Peptidases are enzymes that hydrolyse peptide bonds. They are necessary for the
survival of all living creatures, and they are encoded by about 2% of genes in all
kinds of organisms. It has been estimated that 14% of the five hundred human
peptidases are under investigation as drug targets (Southan, 2001). Peptidases
are important for many biological processes including digestion of food proteins,
recycling of intracellular proteins, the blood coagulation cascade, antigen presen-
tation, and activation of a variety of proteins, including enzymes, peptide hormones,
and neurotransmitters. We calculate that 18% of all proteins in the SwissProt
protein sequence database are annotated as undergoing post-translational proteolytic
processing during maturation.
There are many industrial uses for peptidases, though often mixtures rather
than purified enzymes are used. The earliest were in cheese making, initially
using plant juices to clot milk (according to Homer in The Iliad, fig juice, which
contains ficain, C01.006, was used) and then ‘rennet’, animal stomach contents that
contain chymosin (A01.006). Peptidases are also used to tenderize meat, clarify
beers and enhance the flavours of cheeses and pet foods. Peptidases are used in
the leather industry to remove hair, and make the leather more supple (“bating”
and “soaking” the leather); however many of these are proprietary products for
which the sequences and organisms of origin are not public. Peptidases are also
widely used in cleaning materials, such as biological washing powders and contact
lens cleaning fluid. Besides being the targets of drugs, peptidases are used in
medicine to remove gastrointestinal parasites (anthelminthics), removal of dead skin
from burn patients (debridement), determination of blood groups, and for relief
161
J. Polaina and A.P. MacCabe (eds.), Industrial Enzymes, 161–179.
© 2007 Springer.
162 RAWLINGS ET AL.
of back pain by digesting the cartilage content of herniated intervertebral discs
(chemonucleolysis). Peptidases are also widely used as reagents in the laboratory for
limited proteolysis of proteins, and for generating the peptides required for protein
sequencing. A more recent laboratory use for peptidases of restricted specificity
has been in the processing of recombinant fusion proteins. For example, the NIa
endopeptidases from tobacco etch virus (C04.004) processes the viral polyprotein at
a specific site: ENLYFQ+G/S. Introducing a fragment of nucleotide sequence that
encodes such a site in the vector between that coding for the proteins (or between
that coding for polyHis and a protein) enables individual proteins to be separated
from the fusion product by addition of the endopeptidase (Kapust et al., 2000).
Examples of uses of peptidases are shown in Table 1; the review by Rao et al., 1998
provides many more examples (Rao et al., 1998).
Peptidases are thus an exceptionally important group of enzymes in biology,
medical research and biotechnology. Since the regulation of the activities of pepti-
dases is obviously crucial, the hundreds of proteins that inhibit them are equally
relevant.
In this chapter we will describe some of the terms relevant to peptidases, then
discuss the various classification methods, with particular reference to that employed
by the MEROPS database. In the MEROPS database a unique identifier is given to
each different peptidase, and whenever a peptidase is mentioned in the text, this
identifier will also be given. This will enable the reader to obtain further information
about each peptidase from the MEROPS database.
2. PEPTIDASE
Peptidase is the term recommended in the Enzyme Nomenclature of the Nomen-
clature Committee of the International Union of Biochemistry and Molecular
Biology (NC-IUBMB) and by the Human Gene Nomenclature Committee, as well
as the MEROPS database for any protein that causes the hydrolysis of peptide bonds.
The fact that “peptidase” already forms the root of the names of the many different
sub-types of peptidases: aminopeptidase, carboxypeptidase, and so on (see below),
leads to a very rational and intuitive system of terminology. It is applicable to the
endopeptidases that act on the internal bonds in proteins and large polypeptides
as well as to the oligopeptidases and exopeptidases that act primarily on smaller
substrates. Peptidases are also known colloquially as proteases, proteinases and
proteolytic enzymes.
2.1. Catalytic Type
The catalytic type of a peptidase relates to the chemical groups responsible for its
catalysis of peptide bond hydrolysis. The six specific catalytic types that are recog-
nised are the serine, threonine, cysteine, aspartic, glutamic and metallo- peptidases.
In peptidases of serine, threonine and cysteine type, the catalytic nucleophile is
the reactive group of an amino acid side chain, either a hydroxyl group (serine
INTRODUCTION TO PEPTIDASES AND THE MEROPS DATABASE 163
Table 1. Commercial uses of peptidases Peptidases are listed in order of MEROPS identifier (MERID)
MERID Name Commercial uses
A01.001 pepsin A Protein sequencing.
A01.006 chymosin Cheese making.
A01.013 mucorpepsin Cheese making.
A01.017 endothiapepsin Cheese making.
A01.020 phytepsin Contributes to the malting of cereal grains.
Forms from Centauria sp. and Cynara sp. have
been used to coagulate milk in cheese making.
A26.001 omptin An engineered variant of omptin has been
proposed as a specific endopeptidase for the
cleavage of recombinant fusion proteins.
C01.001 papain Used in food processing.
C01.002 chymopapain Contact-lens cleaning fluid. Stem cell isolation.
Treatment of herniated intervertebral disk.
C01.004 glycyl endopeptidase Protein sequencing.
C01.005 stem bromelain Blood group determination.
C01.006 ficain Blood group determination.
C01.026 ananain Burn debridement.
C01.086 aminopeptidase C Cheese making.
C04.001 nuclear-inclusion-A
endopeptidase (plum pox virus)
Processing of recombinant fusion proteins.
C04.003 tobacco vein mottling virus-type
NIa endopeptidase
Processing of recombinant fusion proteins.
C04.004 tobacco etch virus NIa
endopeptidase
Processing of recombinant fusion proteins.
C15.001 pyroglutamyl-peptidase I
(prokaryote)
Removal of pyroglutamyl groups from
peptides, in protein sequencing. Laboratory use
in identification of group A streptococci and
enterococci.
M09.001 microbial collagenase (Vibrio
sp.)
Several proposed uses, including tissue cell
dispersion, burn debridement.
M09.002 collagenase colA Many uses, including tissue cell dispersion.
M11.001 gametolysin Use in preparation of Chlamydomonas
protoplasts.
M12.066 flavastacin Specificity is similar to that of an
endopeptidase sold for protein sequencing as
‘endoproteinase Asp-N’.
M12.151 ecarin Laboratory use in haematology.
M12.158 russellysin Laboratory use in haematology.
M20.001 glutamate carboxypeptidase Glutamate carboxypeptidase has been
the subject of considerable research in
experimental prodrug strategies for cancer
therapy including ‘antibody-directed enzyme
prodrug therapy’ (ADEPT).
M22.001 O-sialoglycoprotein
endopeptidase
Reagent in study of mammalian cell surface
sialoglycoproteins.
(Continued)