Summary: 3C cysteine protease (picornain 3C)
3C cysteine protease (picornain 3C) Provide feedback
Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral 3C cysteine protease.
Matthews DA, Smith WW, Ferre RA, Condon B, Budahazi G, Sisson W, Villafranca JE, Janson CA, McElroy HE, Gribskov CL, et al; , Cell 1994;77:761-771.: Structure of human rhinovirus 3C protease reveals a trypsin- like polypeptide fold, RNA-binding site, and means for cleaving precursor polyprotein. PUBMED:7515772 EPMC:7515772
Internal database links
|SCOOP:||Peptidase_C4 Pico_P2A Peptidase_S7 Peptidase_S39 Peptidase_S32 Peptidase_S46 Peptidase_C3G Trypsin_2 ATPgrasp_TupA|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR000199
In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
- 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-, N-, 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.
- Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases.
In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.
Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad [PUBMED:11517925].
This signature defines cysteine peptidases belong to MEROPS peptidase family C3 (picornain, clan PA(C)), subfamilies C3A and C3B. The protein fold of this peptidase domain for members of this family resembles that of the serine peptidase, chymotrypsin [PUBMED:8164744], the type example for clan PA.
Picornaviral proteins are expressed as a single polyprotein which is cleaved by the viral C3 cysteine protease. The poliovirus polyprotein is selectively cleaved between the Gln-|-Gly bond. In other picornavirus reactions Glu may be substituted for Gln, and Ser or Thr for Gly.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||cysteine-type endopeptidase activity (GO:0004197)|
|Biological process||proteolysis (GO:0006508)|
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
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This clan contains a diverse set of peptidases with the trypsin fold.
The clan contains the following 24 members:DUF1986 DUF31 DUF316 Peptidase_C24 Peptidase_C3 Peptidase_C30 Peptidase_C37 Peptidase_C3G Peptidase_C4 Peptidase_C62 Peptidase_S29 Peptidase_S3 Peptidase_S30 Peptidase_S31 Peptidase_S32 Peptidase_S39 Peptidase_S46 Peptidase_S55 Peptidase_S6 Peptidase_S7 Peptidase_S76 Pico_P2A Trypsin Trypsin_2
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
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Key: available, not generated, — not available.
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Curation and family details
|Number in seed:||6|
|Number in full:||5564|
|Average length of the domain:||138.60 aa|
|Average identity of full alignment:||48 %|
|Average coverage of the sequence by the domain:||11.31 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||16|
|Download:||download the raw HMM for this family|
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There is 1 interaction for this family. More...
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Peptidase_C3 domain has been found. There are 96 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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