3AGO

Crystal Structure of Ustilago sphaerogena Ribonuclease U2 complexed with adenosine 3'-monophosphate

Summary for 3AGO

• Entry DOI: 10.2210/pdb3ago/pdb
• Related: 1RTU 3AGN
• Descriptor: Ribonuclease U2, [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: purine-specific endo-ribonuclease, hydrolase
• Biological source: Ustilago sphaerogena (Smut fungus)
• Total number of polymer chains: 1
• Total formula weight: 12854.92

Authors

Noguchi, S. (deposition date: 2010-04-03, release date: 2010-07-07, Last modification date: 2024-10-30)

Primary citation

Noguchi, S.
Isomerization mechanism of aspartate to isoaspartate implied by structures of Ustilago sphaerogena ribonuclease U2 complexed with adenosine 3'-monophosphate
Acta Crystallogr.,Sect.D, 66:843-849, 2010

PubMed 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.

PubMed: 20606265
DOI: 10.1107/S0907444910019621

Experimental method

X-RAY DIFFRACTION (0.99 Å)