3AHS

Crystal Structure of Ustilago sphaerogena Ribonuclease U2B

Summary for 3AHS

• Entry DOI: 10.2210/pdb3ahs/pdb
• Related: 1RTU 3AGN 3AGO 3AHW
• Descriptor: Ribonuclease U2, PHOSPHATE ION, POTASSIUM ION, ... (5 entities in total)
• Functional Keywords: purine-specific endo-ribonuclease, hydrolase, isoaspartate
• Biological source: Ustilago sphaerogena (Smut fungus)
• Total number of polymer chains: 3
• Total formula weight: 37726.52

Authors

Noguchi, S. (deposition date: 2010-04-29, release date: 2010-07-07, Last modification date: 2024-10-23)

Primary citation

Noguchi, S.
Structural changes induced by the deamidation and isomerization of asparagine revealed by the crystal structure of Ustilago sphaerogena ribonuclease U2B
Biopolymers, 93:1003-1010, 2010

PubMed Abstract: Under physiological conditions, the deamidation and isomerization of asparagine to isoaspartate (isoAsp) proceeds nonenzymatically via succinimide. Although a large number of proteins have been reported to contain isoAsp, information concerning the three-dimensional structure of proteins containing isoaspartate is still limited. We have crystallized isoAsp containing Ustilago sphaerogena ribonuclease U2B, and determined the crystal structure at 1.32 Å resolution. The structure revealed that the formation of isoAsp32 induces a single turn unfolding of the α-helix from Asp29 to Asp34, and the region from Asp29 to Arg35 forms a U-shaped loop structure. The electron density map shows that isoAsp32 retained the L-configuration at the C(α) atom. IsoAsp32 is in gauche conformation about a C(α)--C(β) bond, and the polypeptide chain bends by ∼90° at isoAsp32. IsoAsp32 protrudes from the surface of the protein, and the abnormal β-peptide bond in the main-chain and α-carboxylate in the side-chain is fully exposed. The structure suggests that the deamidation of the Asn and the isoAsp formation in proteins could confer immunogenicity.

PubMed: 20623666
DOI: 10.1002/bip.21514

Experimental method

X-RAY DIFFRACTION (1.32 Å)