L-rhamnonate dehydratase

 

L-rhamnonate dehydratase is a member of the enolase superfamily that catalyses the syn dehydration of L-rhamnonate. It belongs to the mandelate racemase/muconate lactonising enzyme family, specifically the RhamD subfamily.

 

Reference Protein and Structure

Sequence
Q8ZNF9 UniProt (4.2.1.90) IPR023444 (Sequence Homologues) (PDB Homologues)
Biological species
Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 (Bacteria) Uniprot
PDB
3d47 - Crystal structure of L-rhamnonate dehydratase from Salmonella typhimurium complexed with Mg and D-malate (1.8 Å) PDBe PDBsum 3d47
Catalytic CATH Domains
3.20.20.120 CATHdb (see all for 3d47)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:4.2.1.90)

L-rhamnonate
CHEBI:58118ChEBI
→
2-dehydro-3-deoxy-L-rhamnonate
CHEBI:58371ChEBI
+
water
CHEBI:15377ChEBI
Alternative enzyme names: L-rhamnonate hydro-lyase,

Enzyme Mechanism

Introduction

His 329, hydrogen-bonded to Asp 302, is positioned to function first as the base that abstracts the 2-proton to generate the stabilised enediolate intermediate. Both the subsequent syn-elimination of the 3-OH to generate an enol intermediate and its ketonisation with overall retention of configuration to generate the product also are catalysed by His 329.

Catalytic Residues Roles

UniProt PDB* (3d47)
Asp226, Glu252, Glu280 Asp226A, Glu252A, Glu280A Forms part of the magnesium binding site. metal ligand
His329 His329A Acts as the general acid/base. It is responsible both for the initial abstraction of the proton alpha to the carboxylate group and the dehydration reaction. proton relay, proton acceptor, proton donor
Asp302 Asp302A Increases the basicity of the active site histidine. increase basicity, modifies pKa, increase acidity
Glu349 Glu349A Helps stabilise the transition states and reactive intermediates formed during the course of the reaction. electrostatic stabiliser
*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, assisted keto-enol tautomerisation, overall reactant used, unimolecular elimination by the conjugate base, dehydration, overall product formed, native state of enzyme regenerated

References

  1. Rakus JF et al. (2008), Biochemistry, 47, 9944-9954. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. DOI:10.1021/bi800914r. PMID:18754693.

Step 1. His329 abstracts the proton alpha to the carboxylate group.

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Catalytic Residues Roles

Residue Roles
Asp226A metal ligand
Glu252A metal ligand
Glu280A metal ligand
Glu349A electrostatic stabiliser
Asp302A increase basicity
His329A proton acceptor

Chemical Components

proton transfer, assisted keto-enol tautomerisation, overall reactant used

Step 2. Water is eliminated in a syn beta elimination with concomitant deprotonation of His329.

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Catalytic Residues Roles

Residue Roles
Asp226A metal ligand
Glu252A metal ligand
Glu280A metal ligand
Glu349A electrostatic stabiliser
Asp302A increase acidity
His329A proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, dehydration, overall product formed

Step 3. His329 abstracts the proton from the hydroxyl group alpha to the carboxylate group, initiating the keto-enol tautomerisation with concomitant deprotonation of the same histidine.

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Catalytic Residues Roles

Residue Roles
Asp302A modifies pKa
Glu349A electrostatic stabiliser
Asp226A metal ligand
Glu252A metal ligand
Glu280A metal ligand
His329A proton donor, proton acceptor, proton relay

Chemical Components

assisted keto-enol tautomerisation, proton transfer, overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. His329 abstracts the proton alpha to the carboxylate group.

Step 2. Water is eliminated in a syn beta elimination with concomitant deprotonation of His329.

Step 3. His329 abstracts the proton from the hydroxyl group alpha to the carboxylate group, initiating the keto-enol tautomerisation with concomitant deprotonation of the same histidine.

Products.

Contributors

Gemma L. Holliday