Structure determination carboxypeptidase

The dimensions of cavities in enzymes differ considerably, depending on their physiological function. In many cases the clefts are occupied by clusters of organized water molecules. Such clusters can be seen in certain X-ray structures of enzymes (e.g., the structure of carboxypeptidase A determined by Lipscomb). If the clefts are deep, as in horse liver alcohol dehydrogenase, a channel for removal of water is present (Branden). 

Several plant proteins have been isolated that inhibit the metalloprotease carboxypeptidase A [205-217] (Table 7), notably potato carboxypeptidase inhibitor PCI [207-217] (Table 7). PCI is a small, cysteine-rich protein with a compact knotted structure determined by 3 disulphide links. The C-terminal region inserts into the active site of the carboxypeptidase. The C-terminal glycine is cleaved and remains trapped in the active site, this representing an example of suicide inactivation [207-216]. 

Stehle, R, Brandt, W., Milkowski, C. and Strack, D. (2006/2007) Structure determinants and substrate recognition of serine carboxypeptidase-like acyltransferases from plant secondary metabolism. FEES Lett., 580, 6366-74 and 581, 164-5. 

Carboxypeptidases (CP), single-chain exo-peptidases that remove successive amino acids from the C-terminal end of peptides and proteins. CPs are highly specific for the side-chain moieties of the amino acids to be cleaved, and are classified into various groups and families. The CP approach is used for the end group analysis in primary structure determination. Normally,... 

Reverter. D. Femandez-Catalan, C. Baumgartner. R. Pfandler, R. Huber, R. Bode, W. Vendrell. J. Holak. T.A. Aviles, F.X. Structure of a novel leech carboxypeptidase inhibitor determined free in solution and in complex with human carboxypeptidase A2. Nat. Struct. Biol. 1999, 7. 322-328. 

Dmitrenok, A., Iwashita, T, Nakajima, T, Sakamoto, B., Namikoshi, M., and Nagai, H. (2006) New cyclic depsipeptides from the green alga Bryopsis species application of a carboxypeptidase hydrolysis reaction to the structure determination. Tetrahedron, 62, 1301-1308. 

Carboxypeptidases are zinc-containing enzymes that catalyze the hydrolysis of polypeptides at the C-terminal peptide bond. The bovine enzyme form A is a monomeric protein comprising 307 amino acid residues. The structure was determined in the laboratory of William Lipscomb, Harvard University, in 1970 and later refined to 1.5 A resolution. Biochemical and x-ray studies have shown that the zinc atom is essential for catalysis by binding to the carbonyl oxygen of the substrate. This binding weakens the C =0 bond by... 

The crystal structure of the HNL isolated from S. bicolor (SbHNL) was determined in a complex with the inhibitor benzoic acid." The folding pattern of SbHNL is similar to that of wheat serine carboxypeptidase (CP-WII)" and alcohol dehydrogenase." A unique two-amino acid deletion in SbHNL, however, is forcing the putative active site residues away from the hydrolase binding site toward a small hydrophobic cleft, thereby defining a completely different active site architecture where the triad of a carboxypeptidase is missing. 

Zinc proteases carboxypeptidase A and thermolysin have been extensively studied in solution and in the crystal (for reviews, see Matthews, 1988 Christianson and Lipscomb, 1989). Both carboxypeptidase A and thermolysin hydrolyze the amide bond of polypeptide substrates, and each enzyme displays specificity toward substrates with large hydrophobic Pi side chains such as phenylalanine or leucine. The exopeptidase carboxypeptidase A has a molecular weight of about 35K and the structure of the native enzyme has been determined at 1.54 A resolution (Rees et ai, 1983). Residues in the active site which are important for catalysis are Glu-270, Arg-127, (liganded by His-69, His-196, and Glu-72 in bidentate fashion), and the zinc-bound water molecule (Fig. 30). 

Many secreted proteins, as well as smaller peptide hormones, are acted upon in the endoplasmic reticulum by tryptases and other serine proteases. They often cut between pairs of basic residues such as KK, KR, or RR.214-216 A substilisin-like protease cleaves adjacent to methionine.217 Other classes of proteases (e.g., zinc-dependent carboxypeptidases) also participate in this processing. Serine carboxypeptidases are involved in processing human prohormones.218 Among the serine carboxypeptidases of known structure is one from wheat219 and carboxypeptidase Y, a vacuolar enzyme from yeast.220 Like the pancreatic metallocarboxypeptidases discussed in Section 4, these enzymes remove one amino acid at a time, a property that has made carboxypeptidases valuable reagents for determination of amino acid sequences. Carboxypeptidases may also be used for modification of proteins by removal of one or a few amino acids from the ends. 

The determination of the crystal structure of carboxypeptidase A and its complex with glycyl-L-tyrosine has been completed to 2.0 A resolution by Lipscomb and coworkes (91). A detailed description of the molecule including a comprehensive discussion of structure-function relations have been presented (91). 

Nilges, M., Gronenborn, A. M., Brunger, A. T. and Clore, G M. (1988). Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints Application to crambin, potato carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng. 2, 27-38. 

The combination of Lewis add and nucleophile activations in 12-14 requires four-membered ring transition states. Interestingly, the mechanism for carboxypeptidase A (CPA) catalyzed hydrolysis of peptides also appears to involve joint Lewis add and nucleophile activations that lead to the formation of a four-membered ring transition state. Christianson and Lipscomb [57] have determined the crystal structure (15) of a ketone bound to CPA. Surprisingly, the ketone is in its hydrated form with both oxygens of the gem-diol bound to the active-site zinc of CPA (Figure 6.12). 

M. Nilges, A. M. Gronenborn, A. T. Brunger, and G. M. Clore, Protein Engin., 2,27 (1988). Determination of Three-Dimensional Structures of Proteins by Simulated Annealing with Interproton Distance Restraints. Application to Crambin, Potato Carboxypeptidase Inhibitor, and Barley Serine Proteinase Inhibitor 2. 

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