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Abstract

The structures of enzymes catalyzing the reactions in central metabolic pathways are generally well conserved as are their catalytic mechanisms. The two types of 3-dehydroquinate dehydratase (DHQase) are therefore most unusual since they are unrelated at the sequence level and they utilize completely different mechanisms to catalyze the same overall reaction. The type I enzymes catalyze a cis-dehydration of 3-dehydroquinate via a covalent imine intermediate, while the type II enzymes catalyze a trans-dehydration via an enolate intermediate. Here we report the three-dimensional structures of a representative member of each type of biosynthetic DHQase. Both enzymes function as part of the shikimate pathway, which is essential in microorganisms and plants for the biosynthesis of aromatic compounds including folate, ubiquinone and the aromatic amino acids. An explanation for the presence of two different enzymes catalyzing the same reaction is presented. The absence of the shikimate pathway in animals makes it an attractive target for antimicrobial agents. The availability of these two structures opens the way for the design of highly specific enzyme inhibitors with potential importance as selective therapeutic agents.

3D Complex: A Structural Classification of Protein Complexes

“…Often, an erroneous Biological Unit in one database is correct in the other. For example, the structure 2dhq, a 3-dehydroquinase composed of 12 identical subunits [37], is found in the correct state in the PQS but has only ten subunits in the PDB Biological Unit. An opposite example is the enzyme MenB from Mycobacterium tuberculosis (1q51), which consists of a homohexamer [38].…”

Identification of Polyketide Inhibitors Targeting 3-Dehydroquinate Dehydratase in the Shikimate Pathway of Enterococcus faecalis

“…Moreover, these residues, and in particular Lys170, are positioned in nearly identically positions in these three homologous structures, despite the absence of bound ligand in the efDHQase structure. Such similarities strongly suggest that efDHQase catalyzes the dehydration reaction via a Schiff base mechanism whereby the terminal amine of efDHQase's Lys170 reversibly reacts with the carbonyl of the substrate [24], [25], [26], [27]. To reinforce this notion, the pre-dehydration covalent intermediate bound to seDHQase is also shown in Figure 5 (green sticks), with its carbonyl carbon in close proximity to efDHQase's Lys170.…”

Discovery of Selective Inhibitors of the Clostridium difficile Dehydroquinate Dehydratase

“…The 3 rd -step of the shikimate pathway involves the conversion of 3-dehydroquinate (DHQ) to 3-dehydroshikimate (DHS). Interestingly, the enzymes that catalyze this reaction, dehydroquinate dehydratases (DHQDs), are represented in bacteria by two different subtypes, I and II [7], [8]. Present in C. difficile , type I DHQDs are ∼30 kDa enzymes that assemble into homodimers [7] and use a Schiff-base intermediate to catalyze the dehydration reaction [9].…”