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Structural principles of the wide substrate specificity of Thermoactinomyces vulgaris carboxypeptidase T. Reconstruction of the carboxypeptidase B primary specificity pocket. 2007

V Kh Akparov, and A M Grishin, and M P Yusupova, and N M Ivanova, and G G Chestukhina
Stepanov Laboratory of Protein Chemistry, Institute of Genetics and Selection of Industrial Microorganisms, 1-yi Dorozhnyi Proezd 1, 117545 Moscow, Russia. vhar@ostrov.net

Site-directed mutagenesis in the active site of Thermoactinomyces vulgaris carboxypeptidase T (CpT), which is capable of hydrolyzing both hydrophobic and positively charged substrates, resulted in five mutants: CpT1 (A243G), CpT2 (D253G/T255D), CpT3 (A243G/D253G/T255D), CpT4 (G207S/A243G/D253G/T255D), and CpT5 (G207S/A243G/T250A/D253G/T255D). These mutants step-by-step reconstruct the primary specificity pocket of carboxypeptidase B (CpB), which is capable of cleaving only positively charged C-terminal residues. All of the mutants retained the substrate specificity of the wild-type CpT. Based on comparison of three-dimensional structures of CpB and the CpT5 model, it was suggested that the lower affinity of CpT5 for positively charged substrates than the affinity of CpB could be caused by differences in nature and spatial location of Leu247 and Ile247 and of His68 and Asp65 residues in CpT and CpB, respectively, and also in location of the water molecule bound with Ala250. An additional hydrophobic region was detected in the CpT active site formed by Tyr248, Leu247, Leu203, Ala243, CH3-group of Thr250, and CO-groups of Tyr248 and Ala243, which could be responsible for binding hydrophobic substrates. Thus, notwithstanding the considerable structural similarity of CpT and pancreatic carboxypeptidases, the mechanisms underlying their substrate specificities are different.

UI MeSH Term Description Entries
D008848 Micromonosporaceae A family of gram-positive, saprophytic bacteria occurring in soil and aquatic environments.
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D002268 Carboxypeptidases Enzymes that act at a free C-terminus of a polypeptide to liberate a single amino acid residue. Carboxypeptidase
D001426 Bacterial Proteins Proteins found in any species of bacterium. Bacterial Gene Products,Bacterial Gene Proteins,Gene Products, Bacterial,Bacterial Gene Product,Bacterial Gene Protein,Bacterial Protein,Gene Product, Bacterial,Gene Protein, Bacterial,Gene Proteins, Bacterial,Protein, Bacterial,Proteins, Bacterial
D013379 Substrate Specificity A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts. Specificities, Substrate,Specificity, Substrate,Substrate Specificities
D043424 Carboxypeptidase B A ZINC-dependent carboxypeptidase primary found in the DIGESTIVE SYSTEM. The enzyme catalyzes the preferential cleavage of a C-terminal peptidyl-L-lysine or arginine. It was formerly classified as EC 3.4.2.2 and EC 3.4.12.3. Procarboxypeptidase B,Protaminase
D057927 Hydrophobic and Hydrophilic Interactions The thermodynamic interaction between a substance and WATER. Hydrophilic Interactions,Hydrophilic and Hydrophobic Interactions,Hydrophilicity,Hydrophobic Interactions,Hydrophobicity,Hydrophilic Interaction,Hydrophilicities,Hydrophobic Interaction,Hydrophobicities,Interaction, Hydrophilic,Interaction, Hydrophobic,Interactions, Hydrophilic,Interactions, Hydrophobic
D019943 Amino Acid Substitution The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties. Amino Acid Substitutions,Substitution, Amino Acid,Substitutions, Amino Acid

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