Conformational Variation Revealed by the Crystal Structure of RNase U2A Complexed with Ca Ion and 2'-Adenylic Acid at 1.03 Å Resolution

Abstract

Asparagine can be non-enzymatically deamidated and isomerized via succinimide to isoaspartate. Thispost-translational modification can potentially alter the physical properties or the function of the parent protein.Asn32 of ribonuclease U2A from Ustilago sphaerogena is known to rapidly deamidate and isomerize in alkalineconditions. The crystal structure of ribonuclease U2A complexed with 2'-adenylic acid and calcium ions wasdetermined at 1.03 Å resolution. In this structure, the region from Asp29 to Asp37 winds around a calcium ion, andthe main-chain of Asn32–Gly33 adopts an extended conformation. Rotation of the side-chain of Asn32 could bringAsn32Cγ into close proximity to Gly33N, in a conformation suitable for succinimide formation. The structuresuggests that in solution the region around Asn32–Gly33 is likely to be in equilibrium between multiple conformers,with the deamidation of Asn32 proceeding when the region adopts an extended conformation.