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1  structure 12  species 0  interactions 221  sequences 9  architectures

Family: Peptidase_C32 (PF05411)

Summary: Equine arteritis virus putative proteinase

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Equine arteritis virus putative proteinase Provide feedback

These proteins are characterised by a region that has been proposed to have peptidase activity involved in viral polyprotein processing in replication.

Literature references

  1. Ziebuhr J, Snijder EJ, Gorbalenya AE; , J Gen Virol 2000;81:853-879.: Virus-encoded proteinases and proteolytic processing in the Nidovirales. PUBMED:10725411 EPMC:10725411

  2. Snijder EJ, Wassenaar AL, Spaan WJ; , J Virol 1992;66:7040-7048.: The 5' end of the equine arteritis virus replicase gene encodes a papainlike cysteine protease. PUBMED:1331507 EPMC:1331507

  3. Snijder EJ, Wassenaar AL, Spaan WJ; , J Virol 1994;68:5755-5764.: Proteolytic processing of the replicase ORF1a protein of equine arteritis virus. PUBMED:8057457 EPMC:8057457

  4. den Boon JA, Faaberg KS, Meulenberg JJ, Wassenaar AL, Plagemann PG, Gorbalenya AE, Snijder EJ; , J Virol 1995;69:4500-4505.: Processing and evolution of the N-terminal region of the arterivirus replicase ORF1a protein: identification of two papainlike cysteine proteases. PUBMED:7769711 EPMC:7769711


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR025773

Arteriviruses are enveloped, positive-stranded RNA viruses and include pathogens of major economic concern to the swine- and horse-breeding industries:

  • Equine arteritis virus (EAV).
  • Porcine reproductive and respiratory syndrome virus (PRRSV).
  • Mice actate dehydrogenase-elevating virus.
  • Simian hemorrhagic fever virus.

The arterivirus replicase gene is composed of two open reading frames (ORFs). ORF1a is translated directly from the genomic RNA, whereas ORF1b can be expressed only by ribosomal frameshifting, yelding a 1ab fusion protein. Both replicase gene products are multidomain precursor proteins which are proteolytically processed into functional nonstructural proteins (nsps) by a complex proteolytic cascade that is directed by four (PRRSV/LDV) or three (EAV) proteinase domains encoded in ORF1a. The arterivirus replicase processing scheme involves the rapid autoproteolytic release of two or three N-terminal nsps (nsp1 (or nsp1alpha/1beta) and nsp2) and the subsequent processing of the remaining polyproteins by the "main protease" residing in nsp4, together resulting in a set of 13 or 14 individual nsps. The arterivirus nsp1 region contains a tandem of papain-like cysteine autoprotease domains (PCPalpha and PCPbeta), but in EAV PCPalpha has lost its enzymatic activity, resulting in the 'merge' of nsp1alpha and nsp1beta into a single nsp1 subunit. Thus, instead of three self-cleaving N-terminal subunits, EAV has two: nsp1 and nsp2. The PCPalpha and PCPbeta domains mediate the nsp1alpha|1beta and nsp1beta|2 cleavages, respectively. The catalytic dyad of PCPalpha and PCPbeta domains is composed of Cys and His residues. In EAV, a Lys residue is found in place of the catalytic Cys residue, which explains the proteolytic deficiency of the EAV PCPalpha domain [PUBMED:7769711, PUBMED:10725411, PUBMED:11172046, PUBMED:20696193]. The PCPalpha and PCPbeta domains form respectively peptidase families C31 and C32.

The PCPalpha and PCPbeta domains have a typical papain fold, which consists of a compact global region containing sequentially connected left (L) and right (R) parts in a so-called standard orientation. The L subdomain of PCPalpha consists of four alpha-helices, while the R subdomain is formed by three antiparallel beta strands [PUBMED:19706710]. The L subdomain of the PCBbeta consists of three alpha-helices, while the R subdomain is formed by four antiparallel beta-strands [PUBMED:20410261]. The Cys and His residues face each other at the L-R interface and form the catalytic centre of the PCPalpha and PCPbeta domains [PUBMED:19706710, PUBMED:20410261].

This entry represents the PCPbeta domain (peptidase C32).

Gene Ontology

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Domain organisation

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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...

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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
(4)
Full
(221)
Representative proteomes NCBI
(270)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(4)
Full
(221)
Representative proteomes NCBI
(270)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Alignment:
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Sequence:
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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
(4)
Full
(221)
Representative proteomes NCBI
(270)
Meta
(0)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
Raw Stockholm Download   Download           Download    
Gzipped 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.

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: Manual
Previous IDs: none
Type: Family
Author: Studholme DJ
Number in seed: 4
Number in full: 221
Average length of the domain: 127.60 aa
Average identity of full alignment: 80 %
Average coverage of the sequence by the domain: 4.95 %

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 22.1 22.1
Trusted cut-off 23.1 24.5
Noise cut-off 21.4 22.0
Model length: 128
Family (HMM) version: 7
Download: download the raw HMM for this family

Species distribution

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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_C32 domain has been found. There are 1 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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