2QA9

Crystal structure of the second tetrahedral intermediates of SGPB at pH 4.2

Summary for 2QA9

• Entry DOI: 10.2210/pdb2qa9/pdb
• Descriptor: Streptogrisin-B, 4-mer peptide DAIY, CHLORIDE ION, ... (7 entities in total)
• Functional Keywords: chymotrypsin-type serine peptidase, second tetrahedral intermediate, tetrapeptide, beta barrels, alpha helix, hydrolase
• Biological source: Streptomyces griseus; More
• Total number of polymer chains: 2
• Total formula weight: 19737.14

Authors

Lee, T.W.,James, M.N.G. (deposition date: 2007-06-14, release date: 2007-12-11, Last modification date: 2024-11-13)

Primary citation

Lee, T.W.,James, M.N.
1.2A-resolution crystal structures reveal the second tetrahedral intermediates of streptogrisin B (SGPB).
Biochim.Biophys.Acta, 1784:319-334, 2008

PubMed Abstract: Streptogrisin B (SGPB) has served as one of the models for studying the catalytic activities of serine peptidases. Here we report its native crystal structures at pH 4.2 at a resolution of 1.18A, and at pH 7.3 at a resolution of 1.23A. Unexpectedly, outstanding electron density peaks occurred in the active site and the substrate-binding region of SGPB in the computed maps at both pHs. The densities at pH 4.2 were assigned as a tetrapeptide, Asp-Ala-Ile-Tyr, whereas those at pH 7.3 were assigned as a tyrosine molecule and a leucine molecule existing at equal occupancies in both of the SGPB molecules in the asymmetric unit. Refinement with relaxed geometric restraints resulted in molecular structures representing mixtures of the second tetrahedral intermediates and the enzyme-product complexes of SGPB existing in a pH-dependent equilibrium. Structural comparisons with the complexes of SGPB with turkey ovomucoid third domain (OMTKY3) and its variants have shown that, upon the formation of the tetrahedral intermediate, residues Glu192A to Gly193 of SGPB move towards the alpha-carboxylate O of residue P1 of the bound species, and adjustments in the side-chain conformational angles of His57 and Ser195 of SGPB favor the progression of the catalytic mechanism of SGPB.

PubMed: 18157955
DOI: 10.1016/j.bbapap.2007.11.012

Experimental method

X-RAY DIFFRACTION (1.18 Å)