Nucleophilic elbow

Lipases belong to the subclass of serine hydrolases, and their structure and reaction mechanism are well understood. Their common a/p-hydrolase enzyme fold is characterized by an a-helix that is connected with a sharp turn, referred to as the nucleophilic elbow, to the middle of a P-sheet array. All lipases possess an identical catalytic triad consisting of an Asp or Gin residue, a His and a nucleophilic Ser [14]. The latter residue is located at the nucleophilic elbow and is found in the middle of the highly conserved Gly—AAl—Ser—AA2—Gly sequence in which amino acids AAl and AA2 can vary. The His residue is spatially located at one side of the Ser residue, whereas at the opposite side of the Ser a negative charge can be stabilized in the so-called oxyanion hole by a series of hydrogen bond interactions. The catalytic mechanism of the class of a/P-hydrolases is briefly discussed below using CALB as a typical example, since this is the most commonly applied lipase in polymerization reactions [15]. 

The three-dimensional structure of NTE has not been experimentally determined, but a homology model of the patatin domain indicates that the active site serine (Ser ) is located on a nucleophilic elbow characteristic of serine hydrolases (Wijeyesakere et al., 2007). Moreover, the model indicates that the catalytic site of NTE consists of a novel Ser-Asp catalytic dyad, as in patatin and mammalian cytosolic phospholipase A2 (CPLA2), rather than the classical catalytic triad (Ser-Asp/Glu-His), as found in many serine hydrolases including AChE. Recently, mutations have been identified in NTE that are associated with motor neuron disease (Rainier et al., 2008). The mutations occur within the catalytic domain of NTE, but it is not yet known if they affect the catalytic function of the enzyme or alter some other property of the protein in order to produce disease. 

For the malonate group to be used for fatty acid synthesis, it must first be transferred from malonyl-CoA to malonyl-ACP by the 32.4-kDa monomeric malonyl-CoA ACP transacy-lase, the product of the fabD gene (Fig. 2). A stable malonyl-serine enzyme intermediate is formed during the course of the FabD reaction, and subsequent nucleophilic attack on this ester by the sulfhydryl of ACP yields malonyl-ACP. The high reactivity of the serine in malonyl-ACP transacylase is due to the active site being composed of a nucleophilic elbow as observed in alpha/beta hydrolases. The serine is hydrogen bonded to His-201 in a fashion similar to serine hydrolases. 

In all of the structural models, the amino acid residues apparently constituting the catalytic triad or involved in covalent catalysis were identified as being adjacent to the core structure with the putative active site nucleophile cysteine located at the elbow of the strand-elbow helix motif. In the class II polyester synthase, the highly conserved histidine residue which functions as a general base catalyst in a/p-hydrolases was functionally replaced by an adjacent histidine residue, which too was close to the core structure. 

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