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Quo vadis, Enzymology?
Quoting a recent paper by Chaitan Khosia (2015; Nature Chem Biol.11:438-41), Enzymology has been a vital link between chemistry and biology in the second half of the twentieth century. Enzymology studies focussed on biocatalysts a.o. finding and understanding structure-function relationships of these molecules. Structural information is mostly obtained from X-ray crystallographic studies, of native or engineered proteins, while functional data is derived from enzyme catalysis studies using native or modified substrates. Nowadays, enzymology is dealing more and more with complex, e.g.in vivo systems. Ending with a statement of Khosia: "...the future of enzymology could depend upon how skilled its practitioners become in saving other life scientists from drowning in their own data."
Some examples of previous work
Structure of soybean lipoxygenase-1 showing the essential FeII/III in the centre of the molecule
Much work has been devoted to soybean lipoxygenase. Lipoxygenases (EC 188.8.131.52) are a family of iron-containing enzymes that catalyse the dioxygenation of polyunsaturated fatty acids in lipids containing a cis,cis-1,4- pentadiene structure. It catalyses the following reaction:
fatty acid + O2 => fatty acid hydroperoxide
Lipoxygenases are found in plants, animals and fungi.
Although little was known about the function of hydroperoxy-fatty acids, interest was triggered by the observation that prostaglandins are produced along similar enzymatic steps (catalysed by cyclooxygenases). Nowadays it is known that secondary products derived from lipoxygenase action play important roles in health and disease (cf lipoxins such as resolvins, protectins).
Among other dioxygenases that have been studied is quercetinase, a copper-containing fungal enzyme involved in the degradation of flavonols such as quercetine.
The structure shown is that of subtilisin Carlsberg from Bacillus subtilis (in red) in complex with the inhibitor eglin C (in grey). Data are taken from the protein databank 1cse.pdb. The inhibitor is required to prevent autoproteolysis during crystallization, but is also providing a good example of the interaction between the protease and protein substrates. As an important industrial enzyme subtilisin has been extensively modified since the early 1980s. For a recent overview of the objectives chosen and what has been achieved, see P.N. Bryan (2000)Biochim.Biophys.Acta1543, 203-222).
Lipases are unique enzymes that can act on hydrophobic substrates in an aqueous environment.
Below structures are shown of lipase from Chromobacterium viscosum (alias Burkholderia glumae), a CLOSED (left) and OPEN (right) form.
The active site (Ser-His-Asp) is located in the center of the molecule shown left above (CLOSED form) being inaccessible to the solvent. When a lipid substrate (trigliceride)is presented to the enzyme a large conformational change takes place (at top right) exposing the active site and an extensive hydrophobic area allowing the enzyme to bind to the lipid-water interface (OPEN form). Most likely the enzyme stays bound to the interface during catalysis in which triglycerides are converted to di- and monoglycerides thereby liberrating free fatty acids.
Lipases and phospholipases are also known to be present in a membrane environment. A particular example is the outer membrane phospholipase (OMPLA) found in gram negative bacteria.
This phospholipase (a beta barrel protein) is embedded in the outer membrane mainly containing lipopolysaccharides (LPS) in the outer leaflet and phospholipids in the inner leaflet. The enzyme becomes active after dimerization. Calcium plays an essential role in catalysis. Each of the two calcium ions (green balls) are bound by both OMPLA monomers such that single OMPLA molecules cannot bind calcium efficiently. Two substrate analogs are shown extending downwards from the calcium ion. These analogs are sandwiched in between the two OMPLA monomers.It is still unknown what triggers the formation of the active OMPLA dimer. Most likely membrane perturbation plays an important role. It should be noted that the active site is oriented towards the outer leaflet of the outer membrane.