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.
Internal database links
|Similarity to PfamA using HHSearch:||Peptidase_C24|
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].
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)|
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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
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Curation and family details
|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 build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||7|
|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_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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