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LTR retroelement-like proteases (PRs, also named here as APs) are proteolytic enzymes that play a key role in the maturation process during which several peptides involved in the life cycle of the retroelement are scissed by this enzyme. LTR retroelement PRs belong to [[Clanaa_all|clan AA]] of aspartic peptidases ([[Literature:62353|Rawlings ''et al.'' 2008]]); they dimerize in their active form and may be encoded as a part of the pol polyprotein, alone or as a part of the gag polyprotein, or in frame with a dUTPase (see [[DUTPase|dUTPase]] section). It is well known that the structural PR homodomain is founded in a core ~90-150 residues long wherein the catalytic DTG motif ([[Literature:85462|Pearl and Blundell 1984]]) is the most prominent feature along with a glycine at the C-terminal end preceded by two hydrophobic residues ([[Literature:58377|Pearl and Taylor 1987]]).

At the primary structure level the most conserved part (core) of all clan peptidases may be divided in six amino acidic patterns constituting a template we have called "DTG/ILG". We introduce this template in a forthcoming study (see the references below) but may be preliminarily compared as a HMM profile via the HMM server of this database.

The "DTG/ILG" template is the primary structure phenotype of a structural supersecondary structure, called "Andreeva’s" template ([[Literature:1876|Andreeva 1991]]) that was previously used to describe pepsins and retropepsin. The "Andreeva’s" template is constituted by the following structural elements: an N-terminal loop (A1), a loop containing the catalytic motif (B1), an α-helix (C1) usually not preserved in retropepsins, a β-hairpin loop (D1), a hairpin loop (A2), a wide loop (B2), an α-helix (C2) towards C-terminal, and a loop (D2), which in empirically characterized retropepsins is substituted by a strand or a helical turn ([[Literature:83261|Wlodawer and Gustchina 2000]];[[Literature:19448| Dunn ''et al.'' 2002]]). These elements are responsible of keep both function and three-dimensional (3D) structure in characterized retropepsins and other characterized [[Clan AA|clan AA]] peptidases ([[Literature:83261|Wlodawer and Gustchina 2000]];[[Literature:19448| Dunn ''et al.'' 2002]]). It has also recently suggested that the structure of the HIV-1 (see the figure below) and other clan AA PRs have a flexibility-assisted mechanism evolutionarily preserved to favor the reactive conformation of the enzyme ([[Literature:59419|Piana, Carloni, and Rothlisberger 2002]]; [[Literature:59418|Piana, Carloni, and Parrinello 2002]]; [[Literature:58912|Perryman, Lin, and McCammon 2004]]).

[[Image:And.gif|center]]

<center>3D-structure of the HIV-1 PR monomer adapted from PDB-file [http://www.ebi.ac.uk/pdbsum/3hvp 3hvp]</center>

[[Category:Retroelements]]

Protease - Revision history

imported>GPbernet at 08:49, 28 September 2011