The Crystal Structure of Glutamyl Endopeptidase from Bacillus intermedius Reveals a Structural Link between Zymogen Activation and Charge Compensation

• Published in: Biochemistry (Easton) 2004-03, Vol.43 (10), p.2784-2791
• Main Authors: Meijers, Rob, Blagova, Elena V, Levdikov, Vladimir M, Rudenskaya, Galina N, Chestukhina, Galina G, Akimkina, Tatiana V, Kostrov, Sergei V, Lamzin, Victor S, Kuranova, Inna P
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Anions - chemistry; Bacillus - enzymology; Bacillus intermedius; Bacterial Proteins - chemistry; Bacterial Proteins - isolation & purification; Binding Sites; Catalytic Domain; Crystallization; Crystallography, X-Ray; Disulfides - chemistry; Enzyme Activation; Enzyme Precursors - chemistry; Enzyme Precursors - isolation & purification; Molecular Sequence Data; Protein Binding; Protein Folding; Serine Endopeptidases - chemistry; Serine Endopeptidases - isolation & purification; Staphylococcus - enzymology; Static Electricity; Streptomyces - enzymology; Structural Homology, Protein; Substrate Specificity
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi035354s

Extracellular glutamyl endopeptidase from Bacillus intermedius (BIEP) is a chymotrypsin-like serine protease which cleaves the peptide bond on the carboxyl side of glutamic acid. Its three-dimensional structure was determined for C2221 and C2 crystal forms of BIEP to 1.5 and 1.75 Å resolution, respectively. The topology of BIEP diverges from the most common chymotrypsin architecture, because one of the domains consists of a β-sandwich consisting of two antiparallel β-sheets and two helices. In the C2 crystals, a 2-methyl-2,4-pentanediol (MPD) molecule was found in the substrate binding site, mimicking a glutamic acid. This enabled the identification of the residues involved in the substrate recognition. The presence of the MPD molecule causes a change in the active site; the interaction between two catalytic residues (His47 and Ser171) is disrupted. The N-terminal end of the enzyme is involved in the formation of the substrate binding pocket. This indicates a direct relation between zymogen activation and substrate charge compensation.