Summary: Peptidase family C4
Peptidase family C4 Provide feedback
This peptidase is present in the nuclear inclusion protein of potyviruses.
Internal database links
|Similarity to PfamA using HHSearch:||Trypsin Peptidase_C3 Peptidase_C62 Trypsin_2|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR001730
Tobacco etch virus (TEV), tomato vein mottling virus (TVMV), and plum pox virus (PPV) are members of the Potyviridae family. The potyvirus genome is a (+) stranded RNA and is translated into a single polyprotein upon infection, which is processed by the virally encoded proteases P1, HC-Pro, and NIa. Most of the cleavage events are performed by NIa (nuclear inclusion protein a) protease (NIa-pro). NIa-pro processes seven sites present in the potyvirus polyprotein, named as A, B, C, D, V, E, and F. NIa-pros obtained from potyviruses have similar structures and functions. The potyvirus NIa-pro has a His-Asp-Cys catalytic triad, which is homologous to the trypsin-like proteases except for Cys replacing Ser. NIa-pros obtained from potyviruses share certain sequence identities; however they recognise distinct amino acid sequences at each recognition sites. Consequently, they cannot recognise the cleavage sites of each other efficiently [PUBMED:18024078]. Nia-pro belongs to peptidase family C4. In addition to the catalytic activity NIa-pro possesses also sequence non-specific RNA-binding activity and RNA polymerase (NIb) binding activity [PUBMED:12377789].
The potyvirus NIa protein contains the following two domains; the VPg domain at the N terminus and the NIa-pro domain at the C terminus [PUBMED:18024078, PUBMED:9356344]. The ~250-amino acid NIaPro domain adopts the characteristic two-domain antiparallel beta-barrel fold that is the hallmark of trypsin-like serine proteases, with the catalytic triad residues His, Asp, and Cys located at the interface between domains [PUBMED:12377789].
This entry represents the NIa-pro domain.
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||cysteine-type peptidase activity (GO:0008234)|
|Biological process||proteolysis (GO:0006508)|
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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
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Curation and family details
|Seed source:||Pfam-B_232 (release 3.0)|
|Number in seed:||39|
|Number in full:||1088|
|Average length of the domain:||226.80 aa|
|Average identity of full alignment:||49 %|
|Average coverage of the sequence by the domain:||9.57 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||14|
|Download:||download the raw HMM for this family|
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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_C4 domain has been found. There are 9 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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