5B62
Crystal structure of N-terminal amidase with Asn-Glu-Ala peptide
Summary for 5B62
| Entry DOI | 10.2210/pdb5b62/pdb |
| Related | 5K5U 5K5V 5K60 5K61 5K62 5K63 5K66 |
| Descriptor | Nta1p, ASN-GLU-ALA (3 entities in total) |
| Functional Keywords | n-end rule, nitrilase superfamily, nta1, hydrolase |
| Biological source | Saccharomyces cerevisiae (strain CEN.PK113-7D) (Baker's yeast) More |
| Total number of polymer chains | 2 |
| Total formula weight | 52382.15 |
| Authors | Kim, M.K.,Oh, S.-J.,Lee, B.-G.,Song, H.K. (deposition date: 2016-05-24, release date: 2017-01-11, Last modification date: 2024-03-20) |
| Primary citation | 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 Cited by 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: 27791147DOI: 10.1073/pnas.1612620113 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (3.042 Å) |
Structure validation
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