1. What is MEROPS ? ● Database of Peptidases and their Inhibitors ● More Specific than Pfam, containing in depth, expert details about each entry ● Hierarchical classification ● Accessed at http://merops.sanger.ac.uk/

2. “SLEDGEHAMMER” PEPTIDASES Peptidases that cleave many bonds in a protein, reducing it to peptides ● Physiological food digestion (pepsin) intracellular protein turnover (proteasome, cathepsin D) tissue remodelling (collagenase 1, gelatinases A and B) ● Pathological parasite invasion (cruzipain) arthritis, emphysema, tumour invasion ● Biotechnological cheese making (chymosin) biological washing powders (subtilisin) meat tenderizer (papain) protein sequencing (trypsin, chymotrypsin, pepsin)

3. “CHISEL” PEPTIDASES Peptidases that cleave just one or two bonds in a protein ● Physiological protein biosynthesis (methionyl aminopeptidase, signal peptidase) apoptosis (caspases, granzyme B) blood coagulation (factor Xa) complement assembly (C1r, C1s) activation of bioactive peptides and hormones (furin, kexin, renin) destruction of bioactive peptides (neprilysin) ● Pathological RNA viral polyprotein processing (retropepsin) DNA virus protein processing (adenain, assemblin) bacterial lethal factors (tetanus, anthrax) Alzheimer’s disease ● Biotechnological Purification of expressed proteins (enteropeptidase, TEV proteinase)

4. The MEROPS hierarchy Clan CDCD C11C11 C13C13 C14C14 C25C25 C50C50 C14.001 human (MER00850) mouse (MER00851) rat (MER00852) pig (MER12113) horse (MER06237) gerbil (MER20111) Family Peptidase Species 37 180 1942 24896

5. THE PEPTIDASE UNIT SOL CH Calpain I CH Calpain 7 CH Calpain 10 CH Peptidase unit (domain II) domain III calcium-binding (domain IV) zinc finger PBH domain MIT domain I IIIIIIV

6. TYPE PEPTIDASES caspase 1 (rat) caspase 1 (human) caspase 2 (human) caspase 9 (human) caspase 3 (dog) E < 0.001 caspase 3 (human) E < 0.001 E > 0.001 TRANSITIVE DIRECT

7. DATA SOURCES ● FastA searches of UniProt ● FastA searches of proteomes from completely sequenced genomes ● TBlastN searches of EMBL ● FastPan searches of human and mouse ESTs ● Sequences in papers

8. The MEROPS hierarchy Clan CDCD C11C11 C13C13 C14C14 C25C25 C50C50 C14.001 human (MER00850) mouse (MER00851) rat (MER00852) pig (MER12113) horse (MER06237) gerbil (MER20111) Family Peptidase Species 37 180 1942 24896

9. ADDING FAMILIES TO CLANS ● Every clan has a type peptidase ● A peptidase family is added to a clan if – a peptidase has a similar tertiary structure to the clan type example, as defined by ● the crystallographers ● DALI (z score > 5.99) ● SCOP – the active site residues are in the same order in the sequence as that of the clan type example

10. The MEROPS hierarchy Clan CDCD C11C11 C13C13 C14C14 C25C25 C50C50 C14.001 human (MER00850) mouse (MER00851) rat (MER00852) pig (MER12113) horse (MER06237) gerbil (MER20111) Family Peptidase Species 37 180 1942 24896

11. WHAT IS A PEPTIDASE? ● Similar substrate specificity (known or predicted) ● Sequence homology from amino to carboxy terminus ● Derived from the same node on a cladogram

12. Inhibitors ● MEROPS also contains information about peptidase inhibitors ● There is a hierarchical classification of inhibitors. ● The design and look of the inhibitor pages is very similar to the peptidase.

13. SUMMARY ● Peptidases are enzymes that are difficult to classify by substrate specificity. The MEROPS database provides an alternative, hierarchical classification by domain structure (CLAN), sequence (FAMILY) and specificity (PEPTIDASE). ● There are no families of hypothetical proteins in MEROPS. ● A family contains peptidases of only one catalytic type. ● A clan, however, can consist of families of peptidases of different catalytic types. ● Homologues can be predicted to be peptidases

14. Further Reading Rawlings ND, Tolle DP, Barrett AJ. MEROPS: the peptidase database. Nucleic Acids Res. 2004 Jan 1;32 Database issue:D160-4. PMID: 14681384 Rawlings ND, Tolle DP, Barrett AJ. Evolutionary families of peptidase inhibitors. Biochem J. 2004 Mar 15; (Pt 3):705-16. Review. PMID: 14705960 Handbook of Proteolyic Enzymes. Neil D. Rawlings et al. Academic Press Or mail: merops@sanger.ac.uk

15. Practical Now go to the following page: http://www.sanger.ac.uk/Users/rdf/EMBO/section4.html