Catalytic mechanism human enzyme structure

Although experimental studies provide significant amounts of information regarding the structure and the catalytic activity of these enzymes, several issues concerning the structure (presence of water in the active site) and the catalytic mechanism remained unresolved. Based on the complete X-ray structure of human plasma GPx (2.9 A resolution) [64], we performed active-site and ONIOM QM MM calculations of structure and reaction mechanism [27, 28, 65],... 

PKSs are characterized by their ability to catalyze the formation of polyketide chains from the sequential condensation of acetate units from malonate thioesters. In plants they produce a range of natural products with varied in vivo and pharmacological properties. PKSs of particular note include acridone synthase, bibenzyl synthase, 2-pyrone synthase, and stilbene synthase (STS). STS forms resveratrol, a plant defense compound of much interest with regard to human health. STS shares high sequence identity with CHS, and is considered to have evolved from CHS more than once. ° Knowledge of the molecular structure of the CHS-like enzymes has allowed direct engineering of CHS and STS to alter their catalytic activities, including the number of condensations carried out (reviewed in Refs. 46, 51, 52). These reviews also present extensive, and superbly illustrated, discussions of CHS enzyme structure and reaction mechanism. 

Carbonic anhydrase II, present in human red blood cells (RBCs), catalyzes the reversible hydration of C02. It is one of the most efficient enzymes and only diffusion-limited in its turnover numbers. The catalytic Zn11 is ligated by three histidine residues and OH this ZnOH+ structure renders the zinc center an efficient nucleophile which is able to attack the C02 molecule and capture it in an adjacent hydrophobic pocket. The catalytic mechanism is shown in Figure 9.5. 

The crystal structure of kynureninase from P. fluorescens was solved in 2004. The enzyme shares the same structural fold as aspartate aminotransferase, but shares low sequence similarity. An active site arginine residue (Arg-375) was identified, which is important in substrate binding. The structure of the human kynureninase, which shows a catalytic preference for 3-hydroxy-kynurenine over L-kynurenine, was solved in 2007. The human enzyme shares the same fold as the P. fluorescens enzyme, and also contains an active site arginine residue (Arg-434). The catalytic mechanism requires two acid/base residues, which have not yet been unambiguously assigned. The hydrolytic cleavage step is believed to proceed via a general base mechanism. ... 

A -glycosylation sites in human proteins and 0-P-GlcNAc/phosphorylation sites respectively. CAZY (http //afmb.cnr-mrs.lr/CAZY/) is a comprehensive database for carbohydrate active enzymes (CAZYmes). CAZYmes are classified into seqnence-derived fanulies (Davis and Henrissat, 2002). They are modular, consisting of one or more catalytic domains in harness with many noncatalytic modules, which often posses a carbohydrate binding functionality. Active-site residues, molecular mechanisms and 3D structures are all conserved within families. 

Analysis of human CE by Northern blot shows a single band of approximately 2.1 kilobases (kb) (Riddles et al. 1991), and three bands of approximately 2-, 3-, and 4.2-kb occurring with hCE-2 (Schwer et al. 1997). The intensities of the 2.1-kb band were liver 3> heart > stomach > testis > kidney = spleen > colon > other tissues. For hCE-2, the 2-kb band was located in liver > colon > small intestine > heart, the 3-kb band in liver > small intestine > colon > heart, and the 4.2-kb band in brain, testis, and kidney only. Analysis of substrate structure versus efficiency for ester (pyrethroid substrates) revealed that the two CEs recognize different structural features of the substrate (i.e., acid, alcohol, etc.). The catalytic mechanism involves the formation of an acyl-enzyme on an active serine. While earlier studies of pyrethroid metabolism were primarily performed in rodents, knowledge of the substrate structure-activity relationships and the tissue distribution of hCEs are critical for predicting the metabolism and pharmacokinetics of pesticides in humans. Wheelock et al. (2003) used a chiral mixture of the fluorescent substrate cyclopro-panecarboxylic acid, 3-(2,2-dichloroethenyl)-2,2-dimethyl-, cyano(6-methoxy-2-naphthalenyl)methyl ester (CAS No. 395645-12-2) to study the hydrolytic activity of human liver microsomes. Microsomal activity against this substrate was considered to be low (average value of ten samples 2.04 0.68 nmol min mg ), when compared to p-nitrophenyl acetate (CAS No. 830-03-5) at 3,700 2,100 mg ... 

To understand the inhibition of a-amylase by peptide inhibitors it is crucial to first understand the native substrate-enzyme interaction. The active site and the reaction mechanism of a-amylases have been identified from several X-ray structures of human and pig pancreatic amylases in complex with carbohydrate-based inhibitors. The structural aspects of proteinaceous a-amylase inhibition have been reviewed by Payan. The sequence, architecture, and structure of a-amylases from mammals and insects are fairly homologous and mechanistic insights from mammalian enzymes can be used to elucidate inhibitor function with respect to insect enzymes. The architecture of a-amylases comprises three domains. Domain A contains the residues responsible for catalytic activity. It complexes a calcium ion, which is essential to maintain the active structure of the enzyme and the presence of a chloride ion close to the active site is required for activation. 

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