Family A11

Family

Summary Holotypes Alignment Tree Genomes Literature

A11A

Summary Holotypes Alignment Tree Genomes Literature

A11B

Summary Holotypes Alignment Tree Genomes Literature

Summary for family A11

NamePeptidase family A11 (Copia transposon endopeptidase family)
Family type peptidaseA11.001 - Copia transposon peptidase (Drosophila melanogaster), MEROPS Accession MER0001329 (peptidase unit: 287-399)
Content of familyPeptidase family A11 contains endopeptidases involved in the processing of polyproteins encoded by retrotransposons.
History Identifier created: Proteolysis in Cell Function, pp13-21, IOS Press, Amsterdam (1997)
Transposable genetic elements or transposons are pieces of DNA that are able to copy and insert themselves into different parts of the genome. Those transposons that use a reverse transcriptase for part of this process are known as retrotransposons. Some retrotransposons, known as LTR-retrotransposons, are very similar to retroviruses except that they have no free living stage, and hence do not encode envelope proteins. Like a retrovirus, an LTR-retrotransposon encodes a polyprotein containing an endopeptidase, however. The endopeptidase is essential for releasing the individual proteins from the polyprotein. Some retrotransposon endopeptidases are very similar to retropepsin (A02.001) and are included in the same family (A2). However, probably because of a high rate of mutation, other retrotransposon endopeptidases are very different in sequence and belong to different families. Family A11 includes endopeptidases related to that of the copia retrotransposon of Drosophila melanogaster.
Catalytic typeAspartic
Active siteThe proteinase is assumed to require dimerization to be active, with each monomer contributing an aspartate to the active site. The aspartates are assumed to bind and activate a water molecule that is the nucleophile in peptide bond hydrolysis. The aspartate occurs in a Asp-Xaa-Gly motif in which Xaa can be Ser, Thr or Asn. A sequence similar to the flap in pepsin, which carries the substrate-binding residues, has not been identified.
Activities and specificitiesThe endopeptidase performs all the cleavages that occur in the polyproteins. Cleavage sites have been identified for the Ty1 retrotransposon of Saccharomyces (Garfinkel et al., 1991). The initial cleavage in the Gag-Pol polyprotein exposes the N-terminus of the endopeptidase and is an essential prerequisite for the other cleavages to occur (Lawler et al., 2001).
InhibitorsNo inhibitors are known.
Molecular structureNo tertiary structure has been solved for any member of the family, but the fold is assumed to be similar to that of retropepsin. Hence family A11 is included in clan AA. The endopeptidase is encoded at the 5" end of the pol gene and occurs in middle of the Gag-Pol polyprotein.
ClanAA
Basis of clan assignmentPredicted active site residues for members of this family and family A1 occur in the motif D-T/S-G.
Distribution of family Bacteria details  
Archaea -  
Protozoa details  
Fungi details  
Plants details  
Animals details  
Viruses details  
Biological functionsTypically, a retrotransposon encodes two genes, which are transcribed and translated as a Gag and a Gag-Pol polyprotein (the latter a result of a programmed ribosome frameshift) in the cytoplasm of the host. The polyproteins and retrotransposon RNA assemble into a virus-like particle where processing of the polyproteins occurs. The released proteins include an integrase and a reverse transcriptase which are required for assembling a new retrotransposon cDNA which is inserted into the genome at a new location.
Statistics for family A11Sequences:3569
Identifiers:6
Identifiers with PDB entries:0
Downloadable files Sequence library (FastA format)
Sequence alignment (FastA format)
Phylogenetic tree (Newick format)
Subfamily A11A
Name Peptidase subfamily A11A
Subfamily type peptidase A11.001 - Copia transposon peptidase (Drosophila melanogaster), MEROPS Accession MER0001329 (peptidase unit: 287-399)
Active site residues D292 
Statistics Sequences: 3128
Identifiers: 5
Identifiers with PDB entries: 0
Other databases PFAM PF01021
PFAM PF13976
Downloadable files Sequence library [FastA format]
Sequence alignment [FastA format]
Phylogenetic tree [Newick format]
Peptidases and Homologues MEROPS ID Structure
Copia transposon peptidaseA11.001-
Tnt1 retrotransposon (plant) peptidaseA11.002-
Evelknievel retrotransposon peptidaseA11.004-
Melmoth transposon peptidaseA11.005-
SIRE-1 peptidaseA11.051-
subfamily A11A non-peptidase homologuesnon-peptidase homologue-
subfamily A11A unassigned peptidasesunassigned-
Subfamily A11B
Name Peptidase subfamily A11B
Subfamily type peptidase A11.003 - Ty1 transposon peptidase (Saccharomyces cerevisiae), MEROPS Accession MER0001331 (peptidase unit: 443-538)
Active site residues D457 
Statistics Sequences: 25
Identifiers: 1
Identifiers with PDB entries: 0
Other databases INTERPRO IPR001042
PANTHER PTHR11439
PFAM PF01021
Downloadable files Sequence library [FastA format]
Sequence alignment [FastA format]
Phylogenetic tree [Newick format]
Peptidases and Homologues MEROPS ID Structure
Ty1 transposon peptidaseA11.003-
subfamily A11B non-peptidase homologuesnon-peptidase homologue-
subfamily A11B unassigned peptidasesunassigned-
Peptidases not assigned to subfamily
Peptidases and Homologues MEROPS ID Structure
family A11 non-peptidase homologuesnon-peptidase homologue-
family A11 unassigned peptidasesunassigned-