Summary for clan CA

Summary Alignment Structure Literature
Clan type peptidaseC01.001 - papain (Carica papaya), MEROPS Accession MER0000647 (peptidase unit: 134-345); PDB accession 1PE6
HistoryBiochem.J. 290:205-218 (1993)
DescriptionCysteine nucleophile; catalytic residues in the order Cys, His, Asn (or Asp) in sequence
Contents of clanClan CA contains several families of cysteine peptidases.
EvidenceClan CA contains all the families of peptidases that are known to have structures similar to that of papain. Other families are assigned to clan CA on the basis of sequence motifs. In addition to the residues Cys158 and His292 of the catalytic dyad, two other functionally important residues are commonly present in papain and its relatives (see the Alignment). These are Gln152 that helps in the formation of the ‘oxyanion hole’, an electrophilic centre that stabilizes the tetrahedral intermediate, and Asn308 (sometimes Asp in families C12, C19, C28 and C39), which is thought to orientate the imidazolium ring of the catalytic His (Polgar, 2004). The order of these residues in the sequence is Gln, Cys, His, Asn/Asp, and in mature papain, the numbering is Gln19, Cys25, His159 and Asn175. Clan CN also contains peptidases with a Cys, His catalytic dyad but with a different fold. There are several families of peptidases that process polyproteins from RNA viruses that also possess a Cys, His catalytic dyad, but cannot at present be assigned to either clan CA or CN.
Catalytic mechanismCatalysis by the clan CA peptidases proceeds through an acyl enzyme intermediate. The roles of His159, Gln19 and Asn175 have been fully reviewed by Polgar (2004).
Peptidase activityMost of the peptidases in clan CA are endopeptidases, but several peptidases in family C1 have predominantly exopeptidase activities (see the family C1 summary). The clan contains a number of families of polyprotein-processing peptidases of RNA viruses, including family C28, which contains the foot-and-mouth disease virus L-peptidase.
Protein foldStructures have been determined for several families in the clan: C1 (papain, Kamphuis etal, 1984), C2 (Hosfield et al., 1999), C6 (Guo et al., 2011), C10 (Kagawa et al., 2000), C12 (Johnston et al., 1997), C16 (Lee et al., 2007), C19 (Hu et al., 2002), C28 (Guarne et al., 1998), C31 (Sun et al., 2009), C32 (Xue et al., 2010), C33 (van Kasteren et al., 2013), C39 (Ishii et al., 2010), C47 (Filipek et al., 2003), C54 (Sugawara et al., 2005), C58 (Zhu et al., 2004), C64 (Komander & Barford, 2008), C65 (Nanao et al., 2004), C66 (Wenig et al., 2004), C67 (Sato et al., 2015), C78 (Ha et al., 2011), C83 (Vivares et al., 2005), C85 (Huang et al., 2012), C86 (Weeks et al., 2011), C87 (Capodagli et al., 2011), C93 (Chatterjee et al., 2012), C100 (Kagawa et al., 2000), C101 (Rivkin et al., 2013), C102 (Kohler et al., 2014) and C104 (McGowan et al., 2012). The fold consists of two domains with the active site between them. One domain consists of a bundle of helices, with the active site Cys at the end of one of them; the second domain is a beta barrel and carries the active site His and Asn (or Asp).
EvolutionIt is very possible that clan CA shares an origin with clan CE, the characteristic folds being related by circular permutation, as is suggested in the SCOP database [sunid 54001]. The sequences of each of the type peptidases (papain, C01.001, and adenain, C05.001) of the two clans contain two sequence motifs that are generally conserved throughout the clans. These motifs contain the key catalytic residues, Cys and His, and are Gln-(Xaa)n1-Cys and His-(Xaa)n2-Asn/Glu (where n1 = 5 or 6 and n2 = 15 or 16), respectively. In clan CA the Cys-motif occurs first in the sequence, followed by the His, whereas the reverse is the case in clan CE. The idea that the two parts of the catalytic site have exchanged positions in a circular permutation during the evolution of the clans is consistent with the protein folds, as can be seen in the three-dimensional and two-dimensional representations of the structures in the MEROPS database.
Homologous non-peptidase familiesNon-peptidase proteins that are homologous with the clan CA peptidases include phytochelatin synthase (Vivares et al., 2005), arylamine N-acetyltransferase (Boukouvala & Fakis, 2005) and coagulation factor XIII transglutaminase (Makarova et al., 1999).
Activation mechanismPapain and many other members of subfamily C1A are synthesized as inactive proenzymes with N-terminal propeptides. In the example of cathepsin B (C01.060) the propeptide blocks access of substrate to the already formed active site (Podobnik et al., 1997). The propeptides are cleaved (often autolytically) to generate the active peptidases. The free propeptides of cathepsins B, L and others remain potent inhibitors of the peptidases (Guay et al., 2000), and with homologues they form family I29. In family C10, the proenzyme of streptopain is also autolytically activated (Chen et al., 2003). In family C2, some calpains are activated by a Ca2+-induced conformational change (Strobl et al., 2000).
Other databases PFAMCL0125
SCOP54001

Families

Family Family Type Peptidase Structure
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
C10 agglutinin peptidase ({Marasmius oreades}) (Marasmius oreades) -
C11 OTULIN peptidase (Homo sapiens) -
C12 GtgE peptidase (Salmonella enterica) -
C14 PlyC phage lysin (Streptococcus phage C1) -
C15 papain-like peptidase 1 alpha (simian hemorrhagic fever virus) (simian hemorrhagic fever virus) -
C110 kyphoscoliosis peptidase (Mus musculus) -
C111 coagulation factor XIIIa (Homo sapiens) -
C113 IgdE peptidase ({Streptococcus suis}) (Streptococcus suis) -
C115 MINDY-1 protein (Homo sapiens) -
C117 SpvD g.p. ({Salmonella enterica}) (Salmonella typhimurium) -
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) -
C39 bacteriocin-processing peptidase (Pediococcus acidilactici) Yes
C47 staphopain A (Staphylococcus aureus) Yes
C51 D-alanyl-glycyl peptidase (staphylococcal phage phi11-type) (Staphylococcus aureus) -
C54 autophagin-1 (Homo sapiens) Yes
C58 YopT peptidase (Yersinia pestis) Yes
C64 Cezanne peptidase (Homo sapiens) -
C65 otubain-1 (Homo sapiens) Yes
C66 IdeS peptidase (Streptococcus pyogenes) Yes
C67 CylD peptidase (Homo sapiens) -
C70 AvrRpt2 peptidase (Pseudomonas syringae) -
C71 pseudomurein endoisopeptidase Pei (Methanobacterium phage psiM2) -
C76 viral tegument protein deubiquitinylating peptidase (human herpesvirus 1) -
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) -
C87 nairovirus deubiquitinylating peptidase (Crimean-Congo hemorrhagic fever virus) Yes
C93 LapG peptidase ({Pseudomonas fluorescens}) (Pseudomonas fluorescens) Yes
C96 McjB peptidase (Escherichia coli) -
C98 USPL1 peptidase (Homo sapiens) -

Distribution of clan CA among Kingdoms of Organisms

FamilyBacteriaArchaeaProtozoaFungiPlantsAnimalsViruses
C1+++++++
C2+-+++++
C6-----++
C10+------
C10+--+---
C11-----+-
C12+------
C14+-----+
C15------+
C110++++-+-
C111+-+--+-
C113+---++-
C115++++++-
C117+------
C12+-++++-
C16------+
C19+++++++
C28------+
C31------+
C32------+
C33------+
C39+++-+++
C47+------
C51+++--++
C54+-++++-
C58+------
C64--+-++-
C65+-++++-
C66+-+----
C67---+-+-
C70+------
C71------+
C76------+
C78--++++-
C83+-++++-
C85+++++++
C86--++++-
C87----+++
C93+--+---
C96+------
C98-----+-
Clan+++++++