Biomedical subjects

N D Rawlings

Publications and source records attributed to N D Rawlings.

At least 19 recordsLinked to original sources

PubMed2001

Evolutionary lines of cysteine peptidases.

The proteolytic enzymes that depend upon a cysteine residue for activity have come from at least seven different evolutionary origins, each of which has produced a group of cysteine peptidases with distinctive structures and properties. We show here that the characteristic molecular topologies of the peptidases in each evolutionary line can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. Clan CA contains the families of papain (C1), calpain (C2), streptopain (C10) and the ubiquitin-specific peptidases (C12, C19), as well as many families of viral cysteine endopeptidases. Clan CD contains the families of clostripain (C11), gingipain R (C25), legumain (C13), caspase-1 (C14) and separin (C50). These enzymes have specificities dominated by the interactions of the S1 subsite. Clan CE contains the families of adenain (C5) from adenoviruses, the eukaryotic Ulp1 protease (C48) and the bacterial YopJ proteases (C55). Clan CF contains only pyroglutamyl peptidase I (C15). The picornains (C3) in clan PA have probably evolved from serine peptidases, which still form the majority of enzymes in the clan. The cysteine peptidase activities in clans PB and CH are autolytic only. In conclusion, we suggest that although almost all the cysteine peptidases depend for activity on catalytic dyads of cysteine and histidine, it is worth noting some important differences that they have inherited from their distant ancestral peptidases.

Animals↗

PubMed2000

MEROPS: the peptidase database.

Important additions have been made to the MEROPS database (http://www.bi.bbsrc.ac.uk/Merops/Merops.htm). These include sequence alignments and cladograms for many of the families of peptidases, and these have proved very helpful in the difficult task of distinguishing the sequences of peptidases that are simply species variants of already known enzymes from those that represent novel enzymes.

Databases, Factual↗

PubMed1999

Tripeptidyl-peptidase I is apparently the CLN2 protein absent in classical late-infantile neuronal ceroid lipofuscinosis.

We report that fragments of amino acid sequence recently described for tripeptidyl-peptidase I (TPP I) show that it is the rat homologue of the human CLN2 gene product that is deficient in classical late-infantile neuronal ceroid lipofuscinosis. This is unexpected, since the CLN2 protein has been thought to be a carboxyl-dependent endopeptidase, but TPP I is an exopeptidase possibly of serine-type.

Amino Acid Sequence↗

PubMed1999

MEROPS: the peptidase database.

The MEROPS database (http://www.bi.bbsrc.ac.uk/Merops/Merops.+ ++htm) provides a catalogue and structure-based classification of peptidases (i.e. all proteolytic enzymes). This is a large group of proteins (approximately 2% of all gene products) that is of particular importance in medicine and biotechnology. An index of the peptidases by name or synonym gives access to a set of files termed PepCards each of which provides information on a single peptidase. Each card file contains information on classification and nomenclature, and hypertext links to the relevant entries in online databases for human genetics, protein and nucleic acid sequence data and tertiary structure. Another index provides access to the PepCards by organism name so that the user can retrieve all known peptidases from a particular species. The peptidases are classified into families on the basis of statistically significant similarities between the protein sequences in the part termed the 'peptidase unit' that is most directly responsible for activity. Families that are thought to have common evolutionary origins and are known or expected to have similar tertiary folds are grouped into clans. The MEROPS database provides sets of files called FamCards and ClanCards describing the individual families and clans. Each FamCard document provides links to other databases for sequence motifs and secondary and tertiary structures, and shows the distribution of the family across the major kingdoms of living creatures. Release 3.03 of MEROPS contains 758 peptidases, 153 families and 22 clans. We suggest that the MEROPS database provides a model for a way in which a system of classification for a functional group of proteins can be developed and used as an organizational framework around which to assemble a variety of related information.

Archaea↗

PubMed1998

Identification of the active site of legumain links it to caspases, clostripain and gingipains in a new clan of cysteine endopeptidases.

We show by site-directed mutagenesis that the catalytic residues of mammalian legumain, a recently discovered lysosomal asparaginycysteine endopeptidase, form a catalytic dyad in the motif His-Gly-spacer-Ala-Cys. We note that the same motif is present in the caspases, aspartate-specific endopeptidases central to the process of apoptosis in animal cells, and also in the families of clostripain and gingipain which are arginyl/lysyl endopeptidases of pathogenic bacteria. We propose that the four families have similar protein folds, are evolutionarily related in clan CD, and have common characteristics including substrate specificities dominated by the interactions of the S1 subsite.

Adhesins, Bacterial↗

PubMed1998

Thimet oligopeptidase: site-directed mutagenesis disproves previous assumptions about the nature of the catalytic site.

Zinc metallopeptidases that contain the His-Glu-Xaa-Xaa-His (HEXXH) motif generally have a third ligand of the metal ion that may be either a Glu residue (in clan MA) or a His residue (in clan MB) (Rawlings and Barrett (1995) Methods Enzymol. 248, 183-228). Thimet oligopeptidase has not yet been assigned to either clan, and both Glu and His residues have been proposed as the third ligand. We mutated candidate ligand residues in the recombinant enzyme and identified Glu, His and Asp residues that are important for catalytic activity and/or stability of the protein. However, neither of the Glu and His residues close to the HEXXH motif that have previously been suggested to be ligands is required for the binding of zinc. We conclude that thimet oligopeptidase is not a member of clan MA or clan MB and it is likely that the enzyme possesses a catalytic site and protein fold different from those identified in any metallopeptidase to date. The definitive identification of the third zinc ligand may well require the determination of the crystallographic structure of thimet oligopeptidase or one of its homologues.

Amino Acid Sequence↗

PubMed1997

Structure of membrane glutamate carboxypeptidase.

Membrane glutamate carboxypeptidase (mGCP) hydrolyses pteroylpoly-gamma-glutamates, methotrexate tri-gamma-glutamate and N-acetyl-aspartyl-alpha-glutamate. The enzyme is thought to be required for intestinal uptake of folate, for the resistance of some tumours to methotrexate, and for the metabolism of N-acetyl-aspartyl-glutamate, an abundant neuropeptide. It has recently been reported that mGCP is a protein also known as prostate-specific membrane antigen, homologous with transferrin receptor. This allows us to predict the domain structure of mGCP. Moreover, we have been able to assign the catalytic domain of mGCP to peptidase family M28, which contains cocatalytic zinc metallopeptidases. On the basis of the known structure of an aminopeptidase in family M28, we predict that Asp377, Asp387, Glu425, Asp453 and His553 are ligands of two atoms of zinc bound in the catalytic site of mGCP, and suggest that the aminopeptidases of Vibrio and Streptomyces can serve as valuable models in the design of inhibitors for this medically important enzyme.

Amino Acid Sequence↗

PubMed1997

A primitive enzyme for a primitive cell: the protease required for excystation of Giardia.

Protozoan parasites of the genus Giardia are one of the earliest lineages of eukaryotic cells. To initiate infection, trophozoites emerge from a cyst in the host. Excystation is blocked by specific cysteine protease inhibitors. Using a biotinylated inhibitor, the target protease was identified and its corresponding gene cloned. The protease was localized to vesicles that release their contents just prior to excystation. The Giardia protease is the earliest known branch of the cathepsin B family. Its phylogeny confirms that the cathepsin B lineage evolved in primitive eukaryotic cells, prior to the divergence of plant and animal kingdoms, and underscores the diversity of cellular functions that this enzyme family facilitates.

Animals↗

PubMed1997

Cloning, isolation, and characterization of mammalian legumain, an asparaginyl endopeptidase.

Legumain is a cysteine endopeptidase that shows strict specificity for hydrolysis of asparaginyl bonds. The enzyme belongs to peptidase family C13, and is thus unrelated to the better known cysteine peptidases of the papain family, C1 (Rawlings, N. D., and Barrett, A. J. (1994) Methods Enzymol. 244, 461-486). To date, legumain has been described only from plants and a blood fluke, Schistosoma mansoni. We now show that legumain is present in mammals. We have cloned and sequenced human legumain and part of pig legumain. We have also purified legumain to homogeneity (2200-fold, 8% yield) from pig kidney. The mammalian sequences are clearly homologous with legumains from non-mammalian species. Pig legumain is a glycoprotein of about 34 kDa, decreasing to 31 kDa on deglycosylation. It is an asparaginyl endopeptidase, hydrolyzing Z-Ala-Ala-Asn-7-(4-methyl)coumarylamide and benzoyl-Asn-p-nitroanilide. Maximal activity is seen at pH 5.8 under normal assay conditions, and the enzyme is irreversibly denatured at pH 7 and above. Mammalian legumain is a cysteine endopeptidase, inhibited by iodoacetamide and maleimides, but unaffected by compound E64 (trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane). It is inhibited by ovocystatin (cystatin from chicken egg white) and human cystatin C with Ki values < 5 nM. We discuss the significance of the discovery of a cysteine endopeptidase of a new family and distinctive specificity in man and other mammals.

Amino Acid Sequence↗

PubMed1996

Dipeptidyl-peptidase II is related to lysosomal Pro-X carboxypeptidase.

The N-terminal amino-acid sequence of pig dipeptidyl-peptidase II (EC 3.4.14.2; DPP II) recently published (Huang, K., Takagaki, M., Kani, K. and Ohkubo, I. (1996) Biochim. Biophys. Acta 1290, 149-156) proves that the enzyme is homologous with lysosomal Pro-X carboxypeptidase (EC 3.4.16.2), and belongs to peptidase family S28 in clan SC. This is consistent with a number of biochemical similarities between these two prolyl bond-cleaving serine peptidases. DPP II is not related to granzymes, as was suggested by Huang et al.

Amino Acid Sequence↗

PubMed1995

Families and clans of serine peptidases.

It has become clear that the proteolytic enzymes that depend upon a serine residue for their catalytic activity belong to many different families of proteins. We have attempted to group these families in "clans." A clan is defined as a group of families the members of which have a common ancestor. That is to say, they are homologous, although some of the similarities are in the "twilight zone" and the relationships cannot be proven by rigorous statistical methods. We believe we can recognize five, or perhaps six, clans of serine peptidases. In view of the separate evolutionary origins of the serine peptidases in different clans, it is not surprising to find that they may differ greatly and that indeed there are few generalizations that can be applied to all serine peptidases. In contrast, the members of a clan commonly have marked similarities.

Amino Acid Sequence↗

PubMed1995