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9  structures 161  species 0  interactions 1088  sequences 30  architectures

Family: Peptidase_C4 (PF00863)

Summary: Peptidase family C4

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Peptidase family C4 Provide feedback

This peptidase is present in the nuclear inclusion protein of potyviruses.

Internal database links

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.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Peptidase_PA (CL0124), which has the following description:

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

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(39)
Full
(1088)
Representative proteomes NCBI
(1336)
Meta
(7)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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HTML View  View             
PP/heatmap 1 View             
Pfam viewer View  View             

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(39)
Full
(1088)
Representative proteomes NCBI
(1336)
Meta
(7)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(39)
Full
(1088)
Representative proteomes NCBI
(1336)
Meta
(7)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Raw Stockholm Download   Download           Download   Download  
Gzipped Download   Download           Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_232 (release 3.0)
Previous IDs: none
Type: Family
Author: Bateman A
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.8 20.8
Trusted cut-off 20.9 20.8
Noise cut-off 20.6 20.7
Model length: 235
Family (HMM) version: 14
Download: download the raw HMM for this family

Species distribution

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

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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