1M21

Crystal structure analysis of the peptide amidase PAM in complex with the competitive inhibitor chymostatin

Summary for 1M21

• Entry DOI: 10.2210/pdb1m21/pdb
• Related: 1M22
• Related PRD ID: PRD_000558
• Descriptor: Peptide Amidase, CHYMOSTATIN (3 entities in total)
• Functional Keywords: protein-inhibitor complex, core: eleven-stranded beta-sheet, covered: double layers of alpha helices on top and bottom, hydrolase, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Stenotrophomonas maltophilia; More
• Total number of polymer chains: 4
• Total formula weight: 108306.00

Authors

Labahn, J.,Neumann, S.,Buldt, G.,Kula, M.-R.,Granzin, J. (deposition date: 2002-06-21, release date: 2002-10-16, Last modification date: 2024-10-16)

Primary citation

Labahn, J.,Neumann, S.,Buldt, G.,Kula, M.-R.,Granzin, J.
An alternative mechanism for amidase signature enzymes
J.MOL.BIOL., 322:1053-1064, 2002

PubMed Abstract: The peptide amidase from Stenotrophomonas maltophilia catalyses predominantly the hydrolysis of the C-terminal amide bond in peptide amides. Peptide bonds or amide functions in amino acid side-chains are not hydrolysed. This specificity makes peptide amidase (Pam) interesting for different biotechnological applications. Pam belongs to the amidase signature (AS) family. It is the first protein within this family whose tertiary structure has been solved. The structure of the native Pam has been determined with a resolution of 1.4A and in complex with the competitive inhibitor chymostatin at a resolution of 1.8A. Chymostatin, which forms acyl adducts with many serine proteases, binds non-covalently to this enzyme.Pam folds as a very compact single-domain protein. The AS sequence represents a core domain that is covered by alpha-helices. This AS domain contains the catalytic residues. It is topologically homologous to the phosphoinositol phosphatase domain. The structural data do not support the recently proposed Ser-Lys catalytic dyad mechanism for AS enzymes. Our results are in agreement with the role of Ser226 as the primary nucleophile but differ concerning the roles of Ser202 and Lys123: Ser202, with direct contact both to the substrate molecule and to Ser226, presumably serves as an acid/bases catalyst. Lys123, with direct contact to Ser202 but no contact to Ser226 or the substrate molecule, most likely acts as an acid catalyst.

PubMed: 12367528
DOI: 10.1016/S0022-2836(02)00886-0

Experimental method

X-RAY DIFFRACTION (1.8 Å)