Chorismate mutase (CM) is a regulatory enzyme (EC 5.4.99.5) required for biosynthesis of the aromatic amino acids phenylalanine and tyrosine. CM catalyzes the Claisen rearrangement of chorismate to prephenate, which can subsequently be converted to precursors of either L-Phe or L-Tyr. In bifunctional enzymes the CM domain can be fused to a prephenate dehydratase (P-protein for Phe biosynthesis), (see <PDOC00671>), to a prephenate dehydrogenase (T-protein, for Tyr biosynthesis), or to 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase (EC 2.5.1.54). Besides these prokaryotic bifunctional enzymes, monofunctional CMs occur in prokaryotes as well as in fungi, plants and nematode worms [1].

The type I or AroH class of CM is represented by Bacillus subtilis aroH, a monofunctional, nonallosteric, homotrimeric enzyme characterized by its pseudo-α/β-barrel 3D structure. Each monomer folds into a 5-stranded mixed β-sheet packed against an α-helix and a 3[10] helix. The core is formed by a closed barrel of mixed β-sheets surrounded by helices (see <PDB:2CHS>). The interfaces between adjacent subunits form three equivalent clefts that harbor the active sites [2].

The type II or AroQ class of CM has a completely different all-helical 3D structure, represented by the CM domain of the bifunctional Escherichia coli P-protein (see <PDB:1ECM>). This type is named after the Enterobacter agglomerans monofunctional CM encoded by the aroQ gene [3]. All CM domains from bifunctional enzymes as well as most monofunctional CMs belong to this class, including archaeal CM.

Eukaryotic CM from plants and fungi form a separate subclass of AroQ, represented by the Baker's yeast allosteric CM. These enzymes show only partial sequence similarity to the prokaryotic CMs due to insertions of regulatory domains, but the helix-bundle topology and catalytic residues are conserved and the 3D structure of the E. coli CM dimer resembles a yeast CM monomer (see <PDB:1CSM>) [1,4,5]. The E. coli P-protein CM domain consists of 3 helices and lacks allosteric regulation. The yeast CM has evolved by gene duplication and dimerization and each monomer has 12 helices. Yeast CM is allosterically activated by Trp and inhibited by Tyr [4].

Some proteins known to contain a chorismate mutase domain:

• Bacillus subtilis CM encoded by the aroH gene, a monofunctional homotrimeric enzyme that is not affected by end-product amino acids and effectors.
• Bacterial P-protein, a bifunctional enzyme composed of two catalytic domains, CM and prephenate dehydratase for biosynthesis of phenylalanine (Phe). A C-terminal domain can be involved in feedback inhibition by Phe.
• Bacterial T-protein, a bifunctional enzyme of two catalytic domains, CM and prephenate dehydrogenase (EC 1.3.1.12) for biosynthesis of tyrosine (Tyr). Both enzyme activities are inhibited by Tyr.
• Bacillus subtilis aroA(G) protein, a bifunctional enzyme composed of two catalytic domains, CM and DAHP synthase.
• Enterobacter agglomerans CM encoded by the aroQ gene, a monofunctional chorismate mutase.
• Yeast CM, a monofunctional CM that is allosterically inhibited by Tyr and Phe and activated by tryptophan, the product from a competing enzyme complex at the branch point of aromatic amino acid biosynthesis [1,4].
• Plant CM, which often occur with different isoenzymes that are differently regulated.

We developed a profile for each structural type of CM domain. Each of the 3 profiles covers the corresponding chorismate mutase domain entirely.