M-CSA Mechanism and Catalytic Site Atlas

3-dehydroquinate dehydratase (type I)

3-dehydroquinate dehydratase catalyses the third step in the biosynthesis of chorismate within the Shikimate pathway which synthesises aromatic compounds as well as in the degradative quinate pathway. It is a type I dehydroquinase which catalyses a cis-dehydration of the hexane ring of 3-dehydroquinate via a covalent imine intermediate (unlike the type II dehydroquinase which catalyses a trans-dehydration via an enolate intermediate). Type I dehydroquinases use a Schiff base mechanism. The pathway is essential in microorganisms and plants for the biosynthesis of compounds such as folate, ubiquinone and aromatic amino acids. The absence of this pathway in animals makes it an attractive target for antimicrobial agents.

Reference Protein and Structure

Sequence: P24670 (4.2.1.10) (Sequence Homologues) (PDB Homologues)
Biological species: Salmonella enterica subsp. enterica serovar Typhi (Bacteria)
PDB: 1qfe - THE STRUCTURE OF TYPE I 3-DEHYDROQUINATE DEHYDRATASE FROM SALMONELLA TYPHI (2.1 Å)
Catalytic CATH Domains: 3.20.20.70 (see all for 1qfe)

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Enzyme Reaction (EC:4.2.1.10)

3-dehydroquinate

CHEBI:32364

→

water

CHEBI:15377

3-dehydroshikimate

CHEBI:16630

Enzyme reaction links: IntEnz ENZYME ExplorEnz

Alternative enzyme names: 3-dehydroquinase, 3-dehydroquinate hydrolase, 5-dehydroquinase, 5-dehydroquinate dehydratase, 5-dehydroquinate hydro-lyase, DHQase, Dehydroquinase, Dehydroquinate dehydratase, 3-dehydroquinate hydro-lyase,

Enzyme Mechanism

Mechanism Proposal 1 ☆☆☆

Summary
Step 1
Step 2
Step 3
Step 4
Step 5
Step 6
Step 7
Step 8
Step 9
Products
All Steps

Introduction

His143 is thought to play a part as a general acid in the formation of a Schiff base: a covalent adduct between the substrate and Lys170 of the enzyme. The role of the Schiff base is to act as an electron sink . It may also play a role in distorting the carbocyclic ring of dehydroquinate to render it more reactive. His143 is then thought to play a role in proton abstraction. Glu86 is positioned to interact with His143 and orientate it in a manner reminiscent of the serine proteases to allow it to act as a general base and abstract the C2 proton. However it is worth noting that recent research has put some doubt on this role. Any attack on the substrate from below is prevented by a beta-hairpin so only cis-elimination is possible.

Catalytic Residues Roles

UniProt	PDB* (1qfe)
His143	His143A	Acts as a general acid/base.	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
Lys170	Lys170A	Acts as the catalytic nucleophile.	covalently attached, hydrogen bond acceptor, hydrogen bond donor, nucleophile, proton acceptor, proton donor, nucleofuge, electron pair acceptor, electron pair donor
Glu86	Glu86A	Acts as a general acid/base	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor

*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file; y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain; C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.

Chemical Components

proton transfer, proton relay, bimolecular nucleophilic addition, overall reactant used, enzyme-substrate complex formation, intermediate formation, inferred reaction step, unimolecular elimination by the conjugate base, dehydration, enzyme-substrate complex cleavage, intermediate collapse, schiff base formed, assisted tautomerisation (not keto-enol), overall product formed, intramolecular elimination, intermediate terminated, native state of enzyme regenerated

References

Leech AP et al. (1998), J Biol Chem, 273, 9602-9607. Re-evaluating the Role of His-143 in the Mechanism of Type I Dehydroquinase from Escherichia coli Using Two-dimensional 1H,13C NMR. DOI:10.1074/jbc.273.16.9602. PMID:9545291.
Tizón L et al. (2015), Org Biomol Chem, 13, 706-716. Irreversible covalent modification of type I dehydroquinase with a stable Schiff base. DOI:10.1039/c4ob01782j. PMID:25370445.
Light SH et al. (2014), Biochemistry, 53, 872-880. Crystal Structures of Type I Dehydroquinate Dehydratase in Complex with Quinate and Shikimate Suggest a Novel Mechanism of Schiff Base Formation. DOI:10.1021/bi4015506. PMID:24437575.
Maneiro M et al. (2014), Biochem J, 462, 415-424. Insights into substrate binding and catalysis in bacterial type I dehydroquinase. DOI:10.1042/bj20140614. PMID:24957267.
Light SH et al. (2013), Protein Sci, 22, 418-424. Reassessing the type I dehydroquinate dehydratase catalytic triad: Kinetic and structural studies of Glu86 mutants. DOI:10.1002/pro.2218. PMID:23341204.
Lee WH et al. (2002), Acta Crystallogr D Biol Crystallogr, 58, 798-804. Comparison of different crystal forms of 3-dehydroquinase from Salmonella typhi and its implication for the enzyme activity. PMID:11976491.
Gourley DG et al. (1999), Nat Struct Biol, 6, 521-525. The two types of 3-dehydroquinase have distinct structures but catalyze the same overall reaction. DOI:10.1038/9287. PMID:10360352.

Step 1. Glu86 deprotonates His143, which deprotonates Lys170, activating it.

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Catalytic Residues Roles

Residue	Roles
Glu86A	hydrogen bond acceptor
His143A	hydrogen bond acceptor, hydrogen bond donor, proton relay
Lys170A	hydrogen bond donor, proton donor
Glu86A	proton acceptor
His143A	proton donor, proton acceptor

Chemical Components

proton transfer, proton relay

Step 2. Lys170 attacks the carbonyl carbon of the substrate in a nucleophilic addition.

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Catalytic Residues Roles

Residue	Roles
Glu86A	hydrogen bond donor
His143A	hydrogen bond acceptor
Lys170A	nucleophile

Chemical Components

ingold: bimolecular nucleophilic addition, overall reactant used, enzyme-substrate complex formation, intermediate formation

Step 3. A proton is transferred from the covalently attached lysine to the newly formed hydroxide.

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Catalytic Residues Roles

Residue	Roles
His143A	hydrogen bond acceptor
Glu86A	hydrogen bond donor
Lys170A	covalently attached, hydrogen bond donor
Lys170A	proton donor

Chemical Components

proton transfer, intermediate formation, inferred reaction step

Step 4. Lys170 initiates an elimination of water (which obtains its proton from His143, which deprotonates Glu86) forming the Schiff base intermediate.

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Catalytic Residues Roles

Residue	Roles
His143A	hydrogen bond donor, hydrogen bond acceptor, proton relay
Lys170A	covalently attached
Glu86A	hydrogen bond donor, proton donor
His143A	proton acceptor, proton donor
Lys170A	electron pair donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, dehydration, enzyme-substrate complex cleavage, intermediate collapse, intermediate formation, proton relay, schiff base formed, inferred reaction step

Step 5. Glu86 deprotonates His143, which deprotonates the intermediate at the carbon adjacent to the covalently bound lysine which acts as an electron sink.

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Catalytic Residues Roles

Residue	Roles
Glu86A	hydrogen bond acceptor
His143A	hydrogen bond acceptor, hydrogen bond donor, proton relay
Lys170A	covalently attached
His143A	proton donor, proton acceptor
Glu86A	proton acceptor
Lys170A	electron pair acceptor

Chemical Components

assisted tautomerisation (not keto-enol), proton transfer, intermediate formation, proton relay

Step 6. Lys170 donates its lone pair of electrons back into the ring, initiating a double bond rearrangement and elimination of water, which obtains its proton from His143, which deprotonates Glu86.

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Catalytic Residues Roles

Residue	Roles
Glu86A	hydrogen bond donor
His143A	hydrogen bond donor, hydrogen bond acceptor, proton relay
Lys170A	covalently attached
Glu86A	proton donor
His143A	proton acceptor, proton donor
Lys170A	electron pair donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, overall product formed, dehydration, enzyme-substrate complex cleavage, intermediate formation, intermediate collapse, proton relay

Step 7. Glu86 deprotonates His143, which deprotonates water, which then attacks the carbon to which Lys170 is covalently attached.

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Catalytic Residues Roles

Residue	Roles
His143A	proton relay, hydrogen bond acceptor, hydrogen bond donor
Glu86A	hydrogen bond acceptor
Lys170A	covalently attached
His143A	proton acceptor, proton donor
Glu86A	proton acceptor
Lys170A	electron pair acceptor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, enzyme-substrate complex formation, intermediate formation, proton relay

Step 8. Lys170 deprotonates the hydroxide, which causes Lys170 to be eliminated and the product to be formed.

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Catalytic Residues Roles

Residue	Roles
Glu86A	hydrogen bond donor
His143A	hydrogen bond acceptor, hydrogen bond donor
Lys170A	hydrogen bond acceptor, proton acceptor, nucleofuge

Chemical Components

ingold: intramolecular elimination, proton transfer, enzyme-substrate complex cleavage, overall product formed, intermediate collapse, intermediate terminated

Step 9. Lys170 deprotonates His143, which deprotonates Glu86 in an inferred step that returns the enzyme to its starting state.

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Catalytic Residues Roles

Residue	Roles
Glu86A	hydrogen bond donor
His143A	hydrogen bond donor, hydrogen bond acceptor, proton relay
Lys170A	hydrogen bond acceptor
His143A	proton acceptor
Glu86A	proton donor
Lys170A	proton acceptor
His143A	proton donor

Chemical Components

proton transfer, native state of enzyme regenerated, proton relay, inferred reaction step