Mannonate dehydratase

 

Characterised enzymes in the mannonate dehydratase family (manD) catalyse the dehydration of mannonate to 2-dehydro-3-deoxy-D-gluconate, as part of the catabolism of D-glucuronate. Generally, genomes that encode a member of the mannonate dehydratase family do not have a UxuA (iron(II)-dependent mannoate dehydratase) homologue. Though UxuA also has the TIM barrel fold, it is not a member of the enolase superfamily. Thus, the enolase superfamily mannonate dehydratase family and the UxuAs are an example of convergent evolution of function.

 

Reference Protein and Structure

Sequence
A4XF23 UniProt (4.2.1.8) IPR034589 (Sequence Homologues) (PDB Homologues)
Biological species
Novosphingobium aromaticivorans DSM 12444 (Bacteria) Uniprot
PDB
2qjj - Crystal structure of D-Mannonate dehydratase from Novosphingobium aromaticivorans (1.8 Å) PDBe PDBsum 2qjj
Catalytic CATH Domains
3.30.390.10 CATHdb 3.20.20.120 CATHdb (see all for 2qjj)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:4.2.1.8)

D-mannonate
CHEBI:17767ChEBI
→
2-dehydro-3-deoxy-D-gluconate
CHEBI:57990ChEBI
+
water
CHEBI:15377ChEBI
Alternative enzyme names: D-mannonate hydrolyase, Altronate hydrolase, Altronic hydro-lyase, Mannonate hydrolyase, Mannonic hydrolase, D-mannonate hydro-lyase,

Enzyme Mechanism

Introduction

Tyr159, hydrogen-bonded to Arg147, is positioned to function as the base that abstracts the proton alpha to the carboxylate group (C2) to generate the stabilised enediolate intermediate. The vinylogous syn-elimination of the 3-OH followed by ketonisation with retention of configuration to generate the 2-keto-3-deoxy-D-gluconate product may be catalysed by Tyr159 and/or His212 (shown as His212 here).

Catalytic Residues Roles

UniProt PDB* (2qjj)
Arg147 Arg147A Modulates the pKa of the catalytic tyrosine residue through a hydrogen bonding network. modifies pKa
Tyr159 Tyr159A Acts as a general acid/base. This residue is appropriately positioned to function as the base that abstracts the proton alpha to the carboxylate group. proton acceptor, proton donor
His212 His212A Acts as a general acid/base. Thought to be the residue responsible for the protonation of the leaving hydroxyl group. proton acceptor, proton donor
Asp210, Glu236, Glu262 Asp210A, Glu236A, Glu262A Forms part of the magnesium binding site. metal ligand
Arg283, Glu339 Arg283A, Glu339A Help stabilise the reactive intermediates and transition states formed during the course of the reaction. electrostatic stabiliser
Trp402 Trp402A Thought to help modulate the pKa of His212. modifies pKa
*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, overall product formed, native state of enzyme regenerated

References

  1. Rakus JF et al. (2007), Biochemistry, 46, 12896-12908. Evolution of enzymatic activities in the enolase superfamily: D-Mannonate dehydratase from Novosphingobium aromaticivorans. DOI:10.1021/bi701703w. PMID:17944491.
  2. Zhang Q et al. (2009), J Bacteriol, 191, 5832-5837. Crystal structures of Streptococcus suis mannonate dehydratase (ManD) and its complex with substrate: genetic and biochemical evidence for a catalytic mechanism. DOI:10.1128/JB.00599-09. PMID:19617363.

Step 1. Tyr159 abstracts the proton alpha from the carboxylate group.

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Catalytic Residues Roles

Residue Roles
Glu339A electrostatic stabiliser
Arg283A electrostatic stabiliser
Trp402A modifies pKa
Arg147A modifies pKa
Glu236A metal ligand
Glu262A metal ligand
Asp210A metal ligand
Tyr159A proton acceptor

Chemical Components

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

Step 2. The intermediate collapses, eliminating a water molecule with concomitant deprotonation of His212.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu339A electrostatic stabiliser
Arg283A electrostatic stabiliser
Trp402A modifies pKa
Arg147A modifies pKa
Glu236A metal ligand
Glu262A metal ligand
Asp210A metal ligand
His212A proton donor

Chemical Components

assisted keto-enol tautomerisation, proton transfer, overall product formed

Step 3. His212 abstracts a proton from the hydroxyl coordinated to the Mg(II) ion in an assisted keto-enol tautomerisation. Tyr159 donates a proton to the intermediate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Arg147A modifies pKa
Trp402A modifies pKa
Arg283A electrostatic stabiliser
Glu339A electrostatic stabiliser
Glu236A metal ligand
Glu262A metal ligand
Asp210A metal ligand
Tyr159A proton donor
His212A proton acceptor

Chemical Components

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

Step 1. Tyr159 abstracts the proton alpha from the carboxylate group.

Step 2. The intermediate collapses, eliminating a water molecule with concomitant deprotonation of His212.

Step 3. His212 abstracts a proton from the hydroxyl coordinated to the Mg(II) ion in an assisted keto-enol tautomerisation. Tyr159 donates a proton to the intermediate.

Products.

Contributors

Gemma L. Holliday