title: Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate.
abstract: Aspartates in proteins are isomerized non-enzymatically to isoaspartate via succinimide in vitro and in vivo. In order to elucidate the mechanism of isoaspartate formation within the Asp45-Glu46 sequence of Ustilago sphaerogena ribonuclease U2 based on three-dimensional structure, crystal structures of ribonuclease U2 complexed with adenosine 3'-monophosphate have been solved at 0.96 and 0.99 A resolution. The crystal structures revealed that the C(gamma) atom of Asp45 is located just beside the main-chain N atom of Glu46 and that the conformation which is suitable for succinimide formation is stabilized by a hydrogen-bond network mediated by water molecules 190, 219 and 220. These water molecules are suggested to promote the formation of isoaspartate via succinimide: in the succinimide-formation reaction water 219 receives a proton from the N atom of Glu46 as a general base and waters 190 and 220 stabilize the tetrahedral intermediate, and in the succinimide-hydrolysis reaction water 219 provides a proton for the N atom of Glu46 as a general acid. The purine-base recognition scheme of ribonuclease U2 is also discussed.
authors.affiliation: Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan. snoguchi@mol.f.u-tokyo.ac.jp
authors.forename: Shuji
authors.initials: S
authors.lastname: Noguchi
mesh_terms: D000249:Adenosine Monophosphate / Q000737:chemistry* / Q000378:metabolism; D001224:Aspartic Acid / Q000737:chemistry* / Q000378:metabolism; D018360:Crystallography, X-Ray; D004722:Endoribonucleases / Q000737:chemistry* / Q000378:metabolism; D026581:Isoaspartic Acid / Q000737:chemistry* / Q000378:metabolism; D007536:Isomerism; D008958:Models, Molecular; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D014588:Ustilago / Q000201:enzymology*
chemical_list: D026581:Isoaspartic Acid; D001224:Aspartic Acid; D000249:Adenosine Monophosphate; D004722:Endoribonucleases; C022544:ribonuclease U2