5B62

Crystal structure of N-terminal amidase with Asn-Glu-Ala peptide

5B62 の概要

• エントリーDOI: 10.2210/pdb5b62/pdb
• 関連するPDBエントリー: 5K5U 5K5V 5K60 5K61 5K62 5K63 5K66
• 分子名称: Nta1p, ASN-GLU-ALA (3 entities in total)
• 機能のキーワード: n-end rule, nitrilase superfamily, nta1, hydrolase
• 由来する生物種: Saccharomyces cerevisiae (strain CEN.PK113-7D) (Baker's yeast); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 52382.15

構造登録者

Kim, M.K.,Oh, S.-J.,Lee, B.-G.,Song, H.K. (登録日: 2016-05-24, 公開日: 2017-01-11, 最終更新日: 2024-03-20)

主引用文献

Kim, M.K.,Oh, S.J.,Lee, B.G.,Song, H.K.
Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway.
Proc. Natl. Acad. Sci. U.S.A., 113:12438-12443, 2016

PubMed Abstract: The first step of the hierarchically organized Arg/N-end rule pathway of protein degradation is deamidation of the N-terminal glutamine and asparagine residues of substrate proteins to glutamate and aspartate, respectively. These reactions are catalyzed by the N-terminal amidase (Nt-amidase) Nta1 in fungi such as Saccharomyces cerevisiae, and by the glutamine-specific Ntaq1 and asparagine-specific Ntan1 Nt-amidases in mammals. To investigate the dual specificity of yeast Nta1 (yNta1) and the importance of second-position residues in Asn/Gln-bearing N-terminal degradation signals (N-degrons), we determined crystal structures of yNta1 in the apo state and in complex with various N-degron peptides. Both an Asn-peptide and a Gln-peptide fit well into the hollow active site pocket of yNta1, with the catalytic triad located deeper inside the active site. Specific hydrogen bonds stabilize interactions between N-degron peptides and hydrophobic peripheral regions of the active site pocket. Key determinants for substrate recognition were identified and thereafter confirmed by using structure-based mutagenesis. We also measured affinities between yNta1 (wild-type and its mutants) and specific peptides, and determined K and k for peptides of each type. Together, these results elucidate, in structural and mechanistic detail, specific deamidation mechanisms in the first step of the N-end rule pathway.

PubMed: 27791147
DOI: 10.1073/pnas.1612620113

実験手法

X-RAY DIFFRACTION (3.042 Å)