Summary: Peptidase A6 family
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Peptidase A6 family Provide feedback
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This tab holds annotation information from the InterPro database.
InterPro entry IPR000696
In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold:
- Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.
- Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases.
In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding.
Aspartic endopeptidases EC of vertebrate, fungal and retroviral origin have been characterised [PUBMED:1455179]. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [PUBMED:10625704] and archaean preflagellin have been described [PUBMED:16983194, PUBMED:14622420].
Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure.
This group of proteins, which include the Nodavirus coat precusor endopeptidases, are aspartic peptidases that belong to the MEROPS peptidase family A6 (clan AB).
Nodaviruses are small, icosahedral viruses, pathogenic to insects and mammals. A virus particle consists of a single virion, within which is packaged two RNA stands, RNA1 and RNA2.Nodavirus coat precursor endopeptidase (also known as protein alpha) is the only protein encoded by RNA2. During the process of virion assembly, this precursor is cleaved into coat proteins beta and gamma. RNA1 encodes two proteins, at least one of which is involved in RNA replication. The relatively uncomplicated nature of their structural protein and RNA constituents make the nodaviruses a good virus model [PUBMED:2116525].
The 3D structure of the capsid protein has been determined by X-ray crystallography to 2.8A resolution [PUBMED:2116525]. The structure contains a beta-barrel domain, with a prominent protrusion composed largely of beta-sheet. This protrusion, together with similar protrusions from neighbouring subunits, forms a prominent trigonal pyramid with quasi-3-fold symmetry [PUBMED:2116525]. Two alpha-helices extend toward the interior of the particle [PUBMED:2116525].
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||aspartic-type endopeptidase activity (GO:0004190)|
|Biological process||proteolysis (GO:0006508)|
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The clan contains a set of viral coat protein families and peptidase A6. The only known peptidase activity is an autolytic cleavage releasing a 44-residue C-terminal fragment. The reaction is very slow and only occurs within the assembled virion. There is debate whether this is actually a true peptidase. The virion with these coat or capsid proteins are icosahedral viruses containing sixty triangular coat protein units, each unit consisting of three proteins. The coat protein consists of two subdomains, an eight-stranded beta-barrel on the surface and a three-helix bundle on the inner face.
The clan contains the following 17 members:Birna_VP2 Bromo_coat Calici_coat Capsid-VNN Circo_capsid Como_LCP CRPV_capsid Cucumo_coat Luteo_coat Nepo_coat Peptidase_A21 Peptidase_A6 Rhv SP2 TT_ORF1 Tymo_coat Viral_coat
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
You can see the alignments as HTML or in three different sequence viewers:
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Curation and family details
|Number in seed:||3|
|Number in full:||9|
|Average length of the domain:||359.20 aa|
|Average identity of full alignment:||60 %|
|Average coverage of the sequence by the domain:||88.70 %|
|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:||11|
|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_A6 domain has been found. There are 40 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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