Regulation of a viral proteinase by a peptide and DNA in one-dimensional space: III. atomic resolution structure of the nascent form of the adenovirus proteinase

• Published in: The Journal of biological chemistry Vol. 288; no. 3; pp. 2081 - 2091
• Main Authors: Baniecki, Mary Lynn, McGrath, William J, Mangel, Walter F
• Format: Journal Article
• Language: English
• Published: United States American Society for Biochemistry and Molecular Biology 18.01.2013
• Subjects: 59; Adenoviruses, Human - enzymology; Adenoviruses, Human - genetics; Amino Acid Sequence; Capsid Proteins - chemistry; Capsid Proteins - genetics; Capsid Proteins - metabolism; Crystallography, X-Ray; Cysteine Endopeptidases - chemistry; Cysteine Endopeptidases - genetics; Cysteine Endopeptidases - metabolism; DNA, Viral - chemistry; DNA, Viral - metabolism; Enzyme Activation; Enzymology; Histidine - chemistry; Histidine - metabolism; Humans; Kinetics; Models, Molecular; Molecular Sequence Data; Protein Binding; Protein Precursors - chemistry; Protein Precursors - genetics; Protein Precursors - metabolism; Protein Structure, Secondary; Protein Structure, Tertiary; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; Thermodynamics; Tyrosine - chemistry; Tyrosine - metabolism
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M112.407429

The adenovirus proteinase (AVP), the first member of a new class of cysteine proteinases, is essential for the production of infectious virus, and here we report its structure at 0.98 Å resolution. AVP, initially synthesized as an inactive enzyme, requires two cofactors for maximal activity: pVIc, an 11-amino acid peptide, and the viral DNA. Comparison of the structure of AVP with that of an active form, the AVP-pVIc complex, reveals why AVP is inactive. Both forms have an α + β fold; the major structural differences between them lie in the β-sheet domain. In AVP-pVIc, the general base His-54 Nδ1 is 3.9 Å away from the Cys-122 Sγ, thereby rendering it nucleophilic. In AVP, however, His-54 Nδ1 is 7.0 Å away from Cys-122 Sγ, too far away to be able to abstract the proton from Cys-122. In AVP-pVIc, Tyr-84 forms a cation-π interaction with His-54 that should raise the pK(a) of His-54 and freeze the imidazole ring in the place optimal for forming an ion pair with Cys-122. In AVP, however, Tyr-84 is more than 11 Å away from its position in AVP-pVIc. Based on the structural differences between AVP and AVP-pVIc, we present a model that postulates that activation of AVP by pVIc occurs via a 62-amino acid-long activation pathway in which the binding of pVIc initiates contiguous conformational changes, analogous to falling dominos. There is a common pathway that branches into a pathway that leads to the repositioning of His-54 and another pathway that leads to the repositioning of Tyr-84.