Lyase (EC 4)

A lyase is an enzyme classified by cleavage through means other than hydrolysis or oxidation. Such reactions commonly eliminate a group to create a double bond or a ring; the reverse direction adds a group across the corresponding structural feature. Lyases form EC class 4, with subclasses organized partly by the bonds affected.^[ref]

The involvement of water alone does not make a reaction hydrolysis. Fumarate hydratase, also called fumarase, interconverts fumarate plus water with the (S) form of malate. In the water-removing direction, it generates the double bond of fumarate. In the reverse direction, water adds across that bond.^[ref] The classification concerns the transformation, not merely whether water appears somewhere in its equation.

An invented bookkeeping example begins with $5\mu \mathrm{mol}$ of (S)-malate. If $3\mu \mathrm{mol}$ undergoes the water-eliminating conversion, $2\mu \mathrm{mol}$ malate remains and $3\mu \mathrm{mol}$ fumarate is formed. No carbon atom is removed from the four-carbon skeleton in this reaction. This is a stipulated extent, not a prediction of the position of chemical equilibrium or the reaction speed.

The distinction can also arise in a multistep reaction. Ribonuclease T1 first produces a cyclic phosphate end by a phosphorus–oxygen lyase step and subsequently hydrolyses that cyclic product. Its classification emphasizes the primary cleavage reaction, even though the overall process also includes hydrolysis.^[ref]

Thus a lyase classification gives useful chemical information but does not uniquely specify a protein's structure, substrate range or physiological role. The actual reaction and its experimentally observed direction remain essential to interpreting the enzyme's name.

Fumarate hydratase, also called fumarase, is the enzyme that reversibly interconverts fumarate plus water with L-malate. The activity is EC4.2.1.2:In the hydration direction, water adds across the carbon-carbon double bond of fumarate. In the reverse direction, water is eliminated. Its lyase classification describes this transformation; the mere presence of water does not make the reaction hydrolysis.^[ref]

For an invented inventory, begin with ten micromoles of fumarate and let six micromoles undergo hydration. Four micromoles of fumarate remain and six micromoles of L-malate form. Each retains a four-carbon skeleton, so the counted carbon inventory remains $4(4+6)=40$ micromoles of carbon atoms. The chosen extent does not determine chemical equilibrium or enzyme kinetics.

A 1995 X-ray crystallography study of Escherichia coli fumarase C found a four-subunit assembly at $2.0\text{A˚}$ resolution. A competitive tungstate derivative helped locate the active site, which included atoms from three of the four protein subunits.^[ref] The example shows why counting subunits and locating a catalytic site are different tasks: several chains can cooperate to build one local reaction environment.

Fumarase C, often designated FumC, is a classII form of fumarate hydratase. It catalyzes reversible hydration of fumarate to L-malate. The protein designation should be tied to an organism: Escherichia coli fumarase C is a well-studied species-specific example, while the broader enzyme-activity name does not specify one protein sequence.^[ref]

The net substrate inventory makes the chemistry explicit:Four carbon atoms remain four; adding water changes hydrogen and oxygen content without changing the total charge. This hydration is chemically distinct from oxidation of L-malate to oxaloacetate. The enzyme accelerates a reversible reaction rather than making its net direction independent of conditions.^[ref]

The1995 X-ray crystallography study of the E.coli enzyme resolved an assembly of four identical protein subunits at2.0Å. Its proposed active site involved contributions from three of the four protein subunits; a local catalytic environment therefore need not lie inside just one polypeptide chain. A1996 follow-up with bound compounds distinguished the catalytic A-site from a nearby second binding site. These experiments also show why observing ligand binding does not by itself identify a catalytic site.^[ref][ref]

Escherichia coli fumarase C is a fumarate hydratase of Escherichia coli, commonly designated FumC. It catalyzes the reversible conversion between fumarate plus water and L-malate in the citric acid cycle. The name identifies a particular enzyme, while the broader activity name can cover related catalysts.^[ref]

The 1995 structure revealed a four-subunit assembly at $2.0\text{A˚}$ resolution, with the active site formed using atoms from three chains.^[ref] Further structures in 1996 used bound inhibitors and poor substrates to distinguish this catalytic A-site from a nearby B-site about $12\text{A˚}$ away. The second site was formed by one subunit rather than three.^[ref]

This gives a concrete interpretation problem for a binding experiment. Detecting a compound somewhere on the protein does not establish that it occupies the catalytic site. Comparing its position with substrate analogues, inhibitory behaviour and the multisubunit geometry supplies additional evidence. Similarly, a change in assembly could affect catalytic activity while retaining the same substrate-contacting amino acid residues. Structure and reaction-rate measurements describe complementary aspects of the working enzyme.