Crystal structure of the CN-hydrolase SA0302 from the pathogenic bacterium Staphylococcus aureus belonging to the Nit and NitFhit Branch of the nitrilase superfamily

• Published in: Journal of biomolecular structure & dynamics 2013-10, Vol.31 (10), p.1057-1065
• Main Authors: Gordon, Roni D., Qiu, Wei, Romanov, Vladimir, Lam, Kim, Soloveychik, Maria, Benetteraj, Diana, Battaile, Kevin P., Chirgadze, Yuri N., Pai, Emil F., Chirgadze, Nickolay Y.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Aminohydrolases - chemistry; Catalysis; Catalytic Domain; CN-hydrolase; Conserved Sequence; Crystallography, X-Ray; Hydrolases - chemistry; Models, Molecular; Molecular Sequence Data; Nit-domain; nitrilase; Protein Conformation; protein family; Protein Multimerization; Sequence Alignment; Staphylococcus aureus; Staphylococcus aureus - enzymology; thioredoxin-like activity
• ISSN: 0739-1102; 1538-0254
• DOI: 10.1080/07391102.2012.719111

The nitrilases include a variety of enzymes with functional specificities of nitrilase, amidase, and hydrolase reactions. The crystal structure of the uncharacterized protein SA0302 from the pathogenic microorganism Staphylococcus aureus is solved at 1.7 Å resolution. The protein contains 261 amino acids and presents a four-layer αββα sandwich with a chain topology similar to that of a few known CN-hydrolase folds. In the crystal, the proteins are arranged as dimers whose monomers are related by a pseudo twofold rotation symmetry axis. Analysis of the sequences and structures of CN-hydrolases with known 3D structures shows that SA0302 definitely is a member of Branch 10 (Nit and NitFhit) of the nitrilase superfamily. Enzyme activities and substrate specificities of members of this branch are not yet characterized, in contrast to those of the members of Branches 1-9. Although the sequence identities between Branch 10 members are rather low, less than 30%, five conserved regions are common in this subfamily. Three of them contain functionally important catalytic residues, and the two other newly characterized ones are associated with crucial intramolecular and intermolecular interactions. Sequence homology of the area near the active site shows clearly that the catalytic triad of SA0302 is Glu41-Lys110-Cys146. We suggest also that the active site includes a fourth residue, the closely located Glu119. Despite an extensive similarity with other Nit-family structural folds, SA0302 displays an important difference. Protein loop 111-122, which follows the catalytic Lys110, is reduced to half the number of amino acids found in other Nit-family members. This leaves the active site fully accessible to solvent and substrates. We have identified conservative sequence motifs around the three core catalytic residues, which are inherent solely to Branch 10 of the nitrilase superfamily. On the basis of these new sequence fingerprints, 10 previously uncharacterized proteins also could be assigned to this hydrolase subfamily. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:19