Crystallographic structure at 1.6-Å resolution of the human adenovirus proteinase in a covalent complex with its 11-amino-acid peptide cofactor:: insights on a new fold

The crystal structure of the human adenovirus proteinase (AVP), a cysteine proteinase covalently bound to its I I-amino-acid peptide cofactor pVIc, has been solved to 1.6-Angstrom resolution with a crystallographic R-factor of 0.136, R-free = 0.179. The fold of AVP-pVIc is new and the structural basis for it is described in detail. The polypeptide chain of AVP folds into two domains. One domain contains a five-strand beta-sheet with two peripheral a-helices; this region represents the hydrophobic core of the protein. A second domain contains the N terminus, several C-terminal a-helices, and a small peripheral anti-parallel beta-sheet. The domains interact through an extended polar interface. pVIc spans the two domains like a strap, its C-terminal portion forming a sixth strand on the beta-sheet. The active site is in a long, deep groove located between the two domains. Portions are structurally similar to the active site of the prototypical cysteine proteinase papain, especially some of the Calpha backbone atoms (r.m.s. deviation of 0.354 Angstrom for 12 Calpha atoms). The active-site nucleophile of AVP, the conserved CYS122, was shown to have a pK(a) of 4.5, close to the pK(a) of 3.0 for the nucleophile of papain, suggesting that a similar ion pair arrangement with His(54) may be present in AVP-pVIc. The interactions between AVP and pVIc include 24 non-beta-strand hydrogen bonds, six p-strand hydrogen bonds and one covalent bond. Of the 204 amino acid residues in AVP, 33 are conserved among the many serotypes of adenovirus, and these aid in forming the active site groove, are involved in substrate specificity or interact between secondary structure elements. (C) 2003 Elsevier Science B.V. All rights reserved.