Clans of Peptidases

A clan contains all the modern-day peptidases that have arisen from a single evolutionary origin of peptidases. It represents one or more families that show evidence of their evolutionary relationship by their similar tertiary structures, or when structures are not available, by the order of catalytic-site residues in the polypeptide chain and often by common sequence motifs around the catalytic residues. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter "P" being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.

Aspartic, Cysteine, Glutamic, Metallo, Asparagine, Mixed, Serine, Threonine, Unknown,
Clans of Aspartic Peptidases
CLAN FAMILY TYPE PEPTIDASE STRUCTURE
AA A1 pepsin A (Homo sapiens) Yes
A2 HIV-1 retropepsin (human immunodeficiency virus 1) Yes
A3 cauliflower mosaic virus-type peptidase (cauliflower mosaic virus) -
A9 spumapepsin (human spumaretrovirus) Yes
A11 Copia transposon peptidase (Drosophila melanogaster) -
A28 DNA-damage inducible protein 1 (Saccharomyces cerevisiae) Yes
A32 PerP peptidase (Caulobacter crescentus) Yes
AC A8 signal peptidase II (Escherichia coli) Yes
AD A22 presenilin 1 (Homo sapiens) Yes
A24 type 4 prepilin peptidase 1 (Pseudomonas aeruginosa) Yes
AE A25 gpr peptidase (Bacillus megaterium) Yes
A31 HybD peptidase (Escherichia coli) Yes
AF A26 omptin (Escherichia coli) Yes
unassigned A5 thermopsin (Sulfolobus acidocaldarius) -
A36 sporulation factor SpoIIGA (Bacillus subtilis) -
A37 sso1175 g.p. (Sulfolobus solfataricus) -
Clans of Cysteine Peptidases
CLAN FAMILY TYPE PEPTIDASE STRUCTURE
CA C1 papain (Carica papaya) Yes
C2 calpain-2 (Homo sapiens) Yes
C6 potato virus Y-type helper component peptidase (potato virus Y) Yes
C10 streptopain (Streptococcus pyogenes) Yes
C12 ubiquitinyl hydrolase-L1 (Homo sapiens) Yes
C16 murine hepatitis coronavirus papain-like peptidase 1 (murine hepatitis virus) Yes
C19 ubiquitin-specific peptidase 14 (Homo sapiens) Yes
C28 foot-and-mouth disease virus L-peptidase (foot-and-mouth disease virus) Yes
C31 porcine reproductive and respiratory syndrome arterivirus-type cysteine peptidase alpha (lactate-dehydrogenase-elevating virus) Yes
C32 equine arteritis virus-type cysteine peptidase (porcine reproductive and respiratory syndrome virus) Yes
C33 equine arteritis virus Nsp2-type cysteine peptidase (equine arteritis virus) Yes
C39 bacteriocin-processing peptidase (Pediococcus acidilactici) Yes
C47 staphopain A (Staphylococcus aureus) Yes
C51 D-alanyl-glycyl peptidase (Staphylococcus aureus) Yes
C54 autophagin-1 (Homo sapiens) Yes
C58 YopT peptidase (Yersinia pestis) Yes
C64 Cezanne peptidase (Homo sapiens) Yes
C65 otubain-1 (Homo sapiens) Yes
C66 IdeS peptidase (Streptococcus pyogenes) Yes
C67 CylD peptidase (Homo sapiens) Yes
C70 AvrRpt2 peptidase (Pseudomonas syringae) -
C71 pseudomurein endoisopeptidase Pei (Methanobacterium phage psiM2) -
C76 viral tegument protein deubiquitinylating peptidase (human herpesvirus 1) Yes
C78 UfSP1 peptidase (Mus musculus) Yes
C83 gamma-glutamylcysteine dipeptidyltranspeptidase (Nostoc sp. PCC 7120) Yes
C85 OTLD1 deubiquitinylating enzyme (Homo sapiens) Yes
C86 ataxin-3 (Homo sapiens) Yes
C87 nairovirus deubiquitinylating peptidase (Crimean-Congo hemorrhagic fever virus) Yes
C93 LapG peptidase (Pseudomonas fluorescens) Yes
C96 McjB peptidase (Escherichia coli) -
C98 USPL1 peptidase (Homo sapiens) -
C100 agglutinin peptidase (Marasmius oreades) Yes
C101 OTULIN peptidase (Homo sapiens) Yes
C102 GtgE peptidase (Salmonella enterica) Yes
C104 PlyC phage lysin (Streptococcus phage C1) Yes
C105 papain-like peptidase 1 alpha (simian hemorrhagic fever virus) -
C110 kyphoscoliosis peptidase (Mus musculus) -
C111 coagulation factor XIIIa (Homo sapiens) Yes
C113 IgdE peptidase (Streptococcus suis) -
C115 MINDY-1 protein (Homo sapiens) -
C117 SpvD g.p. (Salmonella typhimurium) Yes
CD C11 clostripain (Clostridium histolyticum) Yes
C13 legumain (Canavalia ensiformis) Yes
C14 caspase-1 (Rattus norvegicus) Yes
C25 gingipain RgpA (Porphyromonas gingivalis) Yes
C50 separase (Saccharomyces cerevisiae) -
C80 RTX self-cleaving toxin (Vibrio cholerae) Yes
C84 prtH peptidase (Tannerella forsythia) -
CE C5 adenain (human adenovirus type 2) Yes
C48 Ulp1 peptidase (Saccharomyces cerevisiae) Yes
C55 YopJ protein (Yersinia pseudotuberculosis) -
C57 vaccinia virus I7L processing peptidase (Vaccinia virus) -
C63 African swine fever virus processing peptidase (African swine fever virus) -
C79 ElaD peptidase (Escherichia coli) -
CF C15 pyroglutamyl-peptidase I (Bacillus amyloliquefaciens) Yes
CL C60 sortase A (Staphylococcus aureus) Yes
C82 L,D-transpeptidase (Enterococcus faecium) Yes
CM C18 hepatitis C virus peptidase 2 (hepatitis C virus) Yes
CN C9 sindbis virus-type nsP2 peptidase (Sindbis virus) Yes
CO C40 dipeptidyl-peptidase VI (Lysinibacillus sphaericus) Yes
CP C97 DeSI-1 peptidase (Mus musculus) Yes
CQ C53 pestivirus Npro peptidase (classical swine fever virus) Yes
unassigned C7 chestnut blight fungus virus p29 peptidase (Cryphonectria hypovirus) -
C8 chestnut blight fungus virus p48 peptidase (Cryphonectria hypovirus 1) -
C21 tymovirus peptidase (turnip yellow mosaic virus) Yes
C23 carlavirus peptidase (apple stem pitting virus) -
C27 rubella virus peptidase (Rubella virus) -
C36 beet necrotic yellow vein furovirus-type papain-like peptidase (beet necrotic yellow vein virus) -
C42 beet yellows virus-type papain-like peptidase (beet yellows virus) -
C75 AgrB peptidase (Staphylococcus aureus) -
C108 Prp peptidase (Staphylococcus aureus) Yes
Clans of Glutamic Peptidases
CLAN FAMILY TYPE PEPTIDASE STRUCTURE
GA G1 scytalidoglutamic peptidase (Scytalidium lignicolum) Yes
GB G2 pre-neck appendage protein (bacteriophage phi-29) Yes
Clans of Metallo Peptidases
CLAN FAMILY TYPE PEPTIDASE STRUCTURE
MA M1 aminopeptidase N (Homo sapiens) Yes
M2 angiotensin-converting enzyme peptidase unit 1 (Homo sapiens) Yes
M3 thimet oligopeptidase (Rattus norvegicus) Yes
M4 thermolysin (Bacillus thermoproteolyticus) Yes
M5 mycolysin (Streptomyces cacaoi) -
M6 immune inhibitor A peptidase (Bacillus thuringiensis) Yes
M7 snapalysin (Streptomyces lividans) Yes
M8 leishmanolysin (Leishmania major) Yes
M9 bacterial collagenase V (Vibrio alginolyticus) Yes
M10 matrix metallopeptidase-1 (Homo sapiens) Yes
M11 gametolysin (Chlamydomonas reinhardtii) -
M12 astacin (Astacus astacus) Yes
M13 neprilysin (Homo sapiens) Yes
M26 IgA1-specific metallopeptidase (Streptococcus sanguinis) -
M27 tentoxilysin (Clostridium tetani) Yes
M30 hyicolysin (Staphylococcus hyicus) -
M32 carboxypeptidase Taq (Thermus aquaticus) Yes
M34 anthrax lethal factor (Bacillus anthracis) Yes
M35 deuterolysin (Aspergillus flavus) Yes
M36 fungalysin (Aspergillus fumigatus) Yes
M41 FtsH peptidase (Escherichia coli) Yes
M43 cytophagalysin (Cytophaga sp.) Yes
M48 Ste24 peptidase (Saccharomyces cerevisiae) Yes
M49 dipeptidyl-peptidase III (Rattus norvegicus) Yes
M54 archaelysin (Methanocaldococcus jannaschii) Yes
M56 BlaR1 peptidase (Staphylococcus aureus) Yes
M57 prtB g.p. (Myxococcus xanthus) -
M60 enhancin (Lymantria dispar nucleopolyhedrovirus) -
M61 glycyl aminopeptidase (Sphingomonas capsulata) -
M64 IgA peptidase (Clostridium ramosum) Yes
M66 StcE peptidase (Escherichia coli) Yes
M72 peptidyl-Asp metallopeptidase (Pseudomonas aeruginosa) -
M76 Atp23 peptidase (Homo sapiens) -
M78 ImmA peptidase (Bacillus subtilis) Yes
M80 Wss1 peptidase (Saccharomyces cerevisiae) -
M84 MpriBi peptidase (Bacillus intermedius) -
M85 NleC peptidase (Escherichia coli) Yes
M90 MtfA peptidase (Escherichia coli) Yes
M91 NleD peptidase (Escherichia coli) -
M93 BACCAC_01431 g.p. and similar (Bacteroides caccae) -
M95 selecase (Methanocaldococcus jannaschii) Yes
M97 EcxAB peptidase (Escherichia coli) Yes
M98 YghJ g.p. (Escherichia coli) -
MC M14 carboxypeptidase A1 (Homo sapiens) Yes
M86 PghP gamma-polyglutamate hydrolase (Bacillus phage phiNIT1) Yes
M99 Csd4 peptidase (Helicobacter pylori) Yes
MD M15 zinc D-Ala-D-Ala carboxypeptidase (Streptomyces albus) Yes
M74 murein endopeptidase (Escherichia coli) Yes
ME M16 pitrilysin (Escherichia coli) Yes
M44 pox virus metallopeptidase (Vaccinia virus) -
MF M17 leucine aminopeptidase 3 (Bos taurus) Yes
MG M24 methionyl aminopeptidase 1 (Escherichia coli) Yes
MH M18 aminopeptidase I (Saccharomyces cerevisiae) Yes
M20 glutamate carboxypeptidase (Pseudomonas sp.) Yes
M28 aminopeptidase S (Streptomyces griseus) Yes
M42 glutamyl aminopeptidase (Lactococcus lactis) Yes
MJ M19 membrane dipeptidase (Homo sapiens) Yes
M38 isoaspartyl dipeptidase (Escherichia coli) Yes
MM M50 site 2 peptidase (Homo sapiens) Yes
MN M55 D-aminopeptidase DppA (Bacillus subtilis) Yes
MO M23 beta-lytic metallopeptidase (Achromobacter lyticus) Yes
MP M67 RPN11 peptidase (Saccharomyces cerevisiae) Yes
MQ M29 aminopeptidase T (Thermus aquaticus) Yes
MS M75 imelysin (Pseudomonas aeruginosa) Yes
MT M81 microcystinase MlrC (Sphingomonas sp. ACM-3962) Yes
unassigned M73 camelysin (Bacillus cereus) -
M77 tryptophanyl aminopeptidase 7-DMATS-type peptidase (Aspergillus fumigatus) Yes
M79 RCE1 peptidase (Saccharomyces cerevisiae) Yes
M82 PrsW peptidase (Bacillus subtilis) -
M87 chloride channel accessory protein 1 (Homo sapiens) -
M88 IMPa peptidase (Pseudomonas aeruginosa) -
M96 Tiki1 peptidase (Homo sapiens) -
Clans of Asparagine Peptide Lyases
CLAN FAMILY TYPE PEPTIDE LYASE STRUCTURE
NA N1 nodavirus peptide lyase (flock house virus) Yes
N2 tetravirus coat protein (Nudaurelia capensis omega virus) Yes
N8 poliovirus capsid VP0-type self-cleaving protein (human poliovirus 1) Yes
NB N6 YscU protein (Yersinia pseudotuberculosis) Yes
NC N7 reovirus type 1 coat protein (Mammalian orthoreovirus 1) Yes
ND N4 Tsh-associated self-cleaving domain and similar (Escherichia coli) Yes
NE N5 picobirnavirus self-cleaving protein (Human picobirnavirus) Yes
Clans of Mixed (C, S, T) Catalytic Type
CLAN FAMILY TYPE PEPTIDASE STRUCTURE
PA C3 poliovirus-type picornain 3C (human poliovirus 1) Yes
C4 nuclear-inclusion-a peptidase (plum pox virus) Yes
C24 rabbit hemorrhagic disease virus 3C-like peptidase (rabbit hemorrhagic disease virus) Yes
C30 porcine transmissible gastroenteritis virus-type main peptidase (transmissible gastroenteritis virus) Yes
C37 calicivirin (Southampton virus) Yes
C62 gill-associated virus 3C-like peptidase (gill-associated virus) -
C74 pestivirus NS2 peptidase (bovine viral diarrhea virus 1) Yes
C99 iflavirus processing peptidase (Ectropis obliqua picorna-like virus) -
C107 alphamesonivirus 3C-like peptidase (Cavally virus) -
S1 chymotrypsin A (Bos taurus) Yes
S3 togavirin (Sindbis virus) Yes
S6 IgA1-specific serine peptidase (Neisseria gonorrhoeae) Yes
S7 flavivirin (yellow fever virus) Yes
S29 hepacivirin (hepatitis C virus) Yes
S30 potyvirus P1 peptidase (plum pox virus) -
S31 pestivirus NS3 polyprotein peptidase (bovine viral diarrhea virus 1) Yes
S32 equine arteritis virus serine peptidase (equine arteritis virus) Yes
S39 sobemovirus peptidase (cocksfoot mottle virus) Yes
S46 dipeptidyl-peptidase 7 (Porphyromonas gingivalis) Yes
S55 SpoIVB peptidase (Bacillus subtilis) -
S64 Ssy5 peptidase (Saccharomyces cerevisiae) -
S65 picornain-like cysteine peptidase (Breda virus) -
S75 White bream virus serine peptidase (White bream virus) -
PB C44 amidophosphoribosyltransferase precursor (Homo sapiens) Yes
C45 acyl-coenzyme A:6-aminopenicillanic acid acyl-transferase precursor (Penicillium chrysogenum) Yes
C59 penicillin V acylase precursor (Lysinibacillus sphaericus) Yes
C69 dipeptidase A (Lactobacillus helveticus) -
C89 acid ceramidase precursor (Homo sapiens) -
C95 lysosomal 66.3 kDa protein (Mus musculus) Yes
P2 EGF-like module containing mucin-like hormone receptor-like 2 (Homo sapiens) Yes
S45 penicillin G acylase precursor (Escherichia coli) Yes
T1 archaean proteasome, beta component (Thermoplasma acidophilum) Yes
T2 glycosylasparaginase precursor (Homo sapiens) Yes
T3 gamma-glutamyltransferase 1 (Escherichia coli) Yes
T7 CwpV self-cleaving threonine peptidase (Peptoclostridium difficile) -
PC C26 gamma-glutamyl hydrolase (Rattus norvegicus) Yes
C56 PfpI peptidase (Pyrococcus furiosus) Yes
S51 dipeptidase E (Escherichia coli) Yes
PD C46 hedgehog protein (Drosophila melanogaster) Yes
N9 intein-containing V-type proton ATPase catalytic subunit A (Saccharomyces cerevisiae) Yes
N10 intein-containing replicative DNA helicase precursor (Synechocystis sp. PCC 6803) Yes
N11 intein-containing chloroplast ATP-dependent peptide lyase (Chlamydomonas eugametos) -
PE P1 DmpA aminopeptidase (Ochrobactrum anthropi) Yes
T5 ornithine acetyltransferase precursor (Saccharomyces cerevisiae) Yes
Clans of Serine Peptidases
CLAN FAMILY TYPE PEPTIDASE STRUCTURE
SB S8 subtilisin Carlsberg (Bacillus licheniformis) Yes
S53 sedolisin (Pseudomonas sp. 101) Yes
SC S9 prolyl oligopeptidase (Sus scrofa) Yes
S10 carboxypeptidase Y (Saccharomyces cerevisiae) Yes
S15 Xaa-Pro dipeptidyl-peptidase (Lactococcus lactis) Yes
S28 lysosomal Pro-Xaa carboxypeptidase (Homo sapiens) Yes
S33 prolyl aminopeptidase (Neisseria gonorrhoeae) Yes
S37 PS-10 peptidase (Streptomyces lividans) -
SE S11 D-Ala-D-Ala carboxypeptidase A (Geobacillus stearothermophilus) Yes
S12 D-Ala-D-Ala carboxypeptidase B (Streptomyces lividans) Yes
S13 D-Ala-D-Ala peptidase C (Escherichia coli) Yes
SF S24 repressor LexA (Escherichia coli) Yes
S26 signal peptidase I (Escherichia coli) Yes
SH S21 cytomegalovirus assemblin (human herpesvirus 5) Yes
S73 gpO peptidase (Enterobacteria phage P2) -
S77 prohead peptidase gp21 (Enterobacteria phage T4) -
S78 prohead peptidase (Enterobacteria phage HK97) -
S80 prohead peptidase gp175 (Pseudomonas phage phiKZ) -
SJ S16 Lon-A peptidase (Escherichia coli) Yes
S50 infectious pancreatic necrosis birnavirus Vp4 peptidase (infectious pancreatic necrosis virus) Yes
S69 Tellina virus 1 VP4 peptidase (Tellina virus 1) Yes
SK S14 peptidase Clp (Escherichia coli) Yes
S41 C-terminal processing peptidase-1 (Escherichia coli) Yes
S49 signal peptide peptidase A (Escherichia coli) Yes
SO S74 Escherichia coli phage K1F endosialidase CIMCD self-cleaving protein (Enterobacteria phage K1F) Yes
SP S59 nucleoporin 145 (Homo sapiens) Yes
SR S60 lactoferrin (Homo sapiens) Yes
SS S66 murein tetrapeptidase LD-carboxypeptidase (Pseudomonas aeruginosa) Yes
ST S54 rhomboid-1 (Drosophila melanogaster) Yes
unassigned S48 HetR putative peptidase (Anabaena variabilis) Yes
S62 influenza A PA peptidase (influenza A virus) Yes
S68 PIDD auto-processing protein unit 1 (Homo sapiens) -
S71 MUC1 self-cleaving mucin (Homo sapiens) Yes
S72 dystroglycan (Homo sapiens) Yes
S79 CARD8 self-cleaving protein (Homo sapiens) Yes
S81 destabilase (Hirudo medicinalis) Yes
Clans of Threonine Peptidases
CLAN FAMILY TYPE PEPTIDASE STRUCTURE
unassigned T8 HopB1 g.p. (Pseudomonas syringae) -
Clans of Peptidases of Unknown Catalytic Type
CLAN FAMILY TYPE PEPTIDASE STRUCTURE
unassigned U32 collagenase (Porphyromonas gingivalis) Yes
U40 protein P5 murein endopeptidase (bacteriophage phi-6) -
U49 Lit peptidase (Escherichia coli) -
U56 homomultimeric peptidase (Thermotoga maritima) Yes
U57 yabG protein (Bacillus subtilis) -
U62 microcin-processing peptidase 1 (Escherichia coli) Yes
U69 AIDA-I self-cleaving autotransporter protein (Escherichia coli) Yes
U72 Dop isopeptidase (Mycobacterium tuberculosis) -
U73 small protease (Pseudomonas aeruginosa) -
U74 neprosin (Nepenthes ventrata) -