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10  structures 351  species 0  interactions 408  sequences 5  architectures

Family: Peptidase_C37 (PF05416)

Summary: Southampton virus-type processing peptidase

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Southampton virus-type processing peptidase Provide feedback

Corresponds to Merops family C37. Norwalk-like viruses (NLVs), including the Southampton virus, cause acute non-bacterial gastroenteritis in humans. The NLV genome encodes three open reading frames (ORFs). ORF1 encodes a polyprotein, which is processed by the viral protease into six proteins.

Literature references

  1. Someya Y, Takeda N, Miyamura T; , J Virol 2002;76:5949-5958.: Identification of active-site amino acid residues in the Chiba virus 3C-like protease. PUBMED:12021327 EPMC:12021327


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001665

Noroviruses (NVs, formerly "Norwalk-like viruses"), which belong to the Caliciviridae, are the major causative agents of nonbacterial acute gastroenteritis in humans. The NV genome, which consists of positive-sense, single-stranded RNA, contains three open reading frames (ORFs). The first ORF produces a polyprotein that is processed by the viral 3C-like protease into six nonstructural proteins. The six NV ORF1 nonstructural proteins are homologous to picornaviral nonstructural proteins and are named accordingly: N-terminal protein, 2C-like nucleoside triphosphatase, 3A-like protein, 3B VPg (genome-linked viral protein), 3C-like protease, and a 3D RNA- dependent RNA polymerase. NV 3C-like proteases are the key enzymes for ORF1 polyprotein processing and also cleave the poly(A)-binding protein, causing cellular translation inhibition. NV 3C-like proteases belong to the chymotrypsin-like protease family, in that they appear to have chymotrypsin-like folds. Whether the 3C-like protease domain has a catalytic dyad of composed of histidine and cysteine or tryad of histidine, glutamate and cysteine remains controversial [PUBMED:16227288, PUBMED:16641296]. The NV 3C-like protease domain forms MEROPS peptidase family C37.

The NV 3C-like protease domain adopts a serine protease-like fold that consists of two beta-barrels separated by a cleft within which lie the active site catalytic residues. The N-terminal beta barrel has two alpha-helices and seven beta-strands. The beta-strands form a twisted antiparallel beta- sheet resembling an incomplete beta-barrel. The core of the incomplete beta- barrel contains hydrophobic residues. The active site histidine residue is found in the N-terminal beta-barrel, as well as the glutamate. The C-terminal six-stranded antiparallel beta-barrel contains the active site cysteine. The catalytic site formed is situated deep within a cleft between the N- and C- terminal beta-barrels [PUBMED:16227288, PUBMED:16641296].

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
(5)
Full
(408)
Representative proteomes NCBI
(397)
Meta
(1)
RP15
(0)
RP35
(0)
RP55
(0)
RP75
(0)
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Format an alignment

  Seed
(5)
Full
(408)
Representative proteomes NCBI
(397)
Meta
(1)
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
(5)
Full
(408)
Representative proteomes NCBI
(397)
Meta
(1)
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

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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.

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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: 5
Number in full: 408
Average length of the domain: 490.50 aa
Average identity of full alignment: 74 %
Average coverage of the sequence by the domain: 30.25 %

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 20.2 20.2
Trusted cut-off 20.2 20.6
Noise cut-off 19.7 20.1
Model length: 535
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_C37 domain has been found. There are 10 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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