Substrate pocket

These results show a clear distortion of substrate binding and catalytic activities upon fragmentation of the multienzymes. The substrate pocket architecture seems to depend on the context of adjacent domains as well. Although questions remain, the linearity rule of NRPS holds in ACV synthetases. Open questions remain on the fate of possibly misactivated amino acids in the terminal... 

Substrate-competitive inhibition is a well known strategy for targeting enzymes, which has been applied successfully in enzyme classes such as the proteases. Nevertheless, its use for kinase inhibition has met with little success. One of the reasons is the rather stretched substrate pocket of kinases. Kinases are likely to use additional binding pockets, which are not located in the immediate environment of the active site [16, 17]. Therefore, kinases lack the specific hydrophobic pockets that could serve as targets for peptidomimetics, as occurs with HIV protease or thrombin. 

Figure 12 The active structure of P450cam with bound camphor. The amino acid side chains that define the substrate pocket and contact the substrate are shown. The dotted line indicates the hydrogen bond between the camphor carbonyl and the phenol side chain of Tyr-96...

Figure 13 The active-site structure of P450bm-3 with palmitoleic acid bound to the substrate pocket. The fatty acid substrate extends along the substrate access channel to the surface of the protein. The side chains lining the channel are also shown...

Ramaswamy, S., M. el Ahmad, O. Danielsson, H. Jornvall and H. Eklund. Crystal structure of cod liver class I alcohol dehydrogenase substrate pocket and structurally variable segments. Protein Sci. 5 663-671, 1996. 

The 1.25 A-crystal structure of the mouse SR in complex with NADP has been solved. The 261 amino acids of the monomer fold into a single domain a//3-structure. A seven-stranded parallel /3-sheet in the center of the molecule is sandwiched by two arrays of three a-helices. The association of two monomers to the active homodimeric SR leads to the formation of a four-helix bundle (Figure 13). Owing to the two-folded crystallographic symmetry of the homodimeric molecule, the parallel /3-sheets in monomer A is in an antiparallel orientation relative to the /3-sheet of monomer B enclosing an angle of 90°. The overall dimensions of the SR dimer are 40 A X 50 A x 80 A. The two substrate pockets bind sepiapterin (or 6-pyruvoyl-tetrahydropterin 42), and the cofactor NADP/NADPH from opposite sides to the enzyme. 

Recently, PI synthesis was accomplished by mutated PLD from Streptomyces anti-bioticus [32], Mutated PLD has a flexible binding substrate pocket that can recognize sterically hindered myo-inositol as a snbstrate. This successful result is supported by the evaluation of the catalytic molecular mechanism of PLD from Streptomyces sp. strain PMF [62], Application of mutagenesis to PLA2 holds considerable promise in the synthesis of novel types of PL containing various functional compounds. 

Figure 11 Generation of immobilized metal catalysts with a substrate pocket by imprinting with a pseudo-substrate (a) attachment of the pseudo-substrate (b) polymerization (c) selective cleavage of the pseudo-substrate (d) removal of the pseudo-substrate and the metal ion (e) addition of the catalytically active metal ion.

Overlaying the structures of the adenine-pocket binding fragments with the substrate-pocket binding fragments revealed that they were separated by about... 

The dark-coloured part in the middle indicates in the upper part the coenzyme binding site the adenine moiety at Au up to the left, the phosphate at Pt , the nicotinamide part at 1 in the middle. The dark sack in the lower part is the substrate pocket. The walls around this pocket contain many amino acid residues with lipophilic side chains, resulting in the enzyme having high affinity for both substrates and competitive inhibitors rich in alkyl groups. 

Fig. 1. Horse liver alcohol dehydrogenase. Peptide chain folding in the two subunits. Fig. 2. Coenzyme and substrate pocket in the ADH molecule (explanation see text).

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