3-dehydro-L-gulonate 2-dehydrogenase

 

2,3-Diketo-L-gulonate reductase (yiaK) is from Escherichia coli. It is the first gene in a nine-gene sequence operon, which is believed to be required for the utilisation of rare sugars for growth. YiaK catalyses the reduction of 2,3-diketo-L-gulonate (DKG) in the presence of NADH to give 3-keto-L-gulonate.

 

Reference Protein and Structure

Sequence
P37672 UniProt (1.1.1.130) IPR023689 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1s20 - A novel NAD binding protein revealed by the crystal structure of E. Coli 2,3-diketogulonate reductase (YiaK) NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ER82 (2.2 Å) PDBe PDBsum 1s20
Catalytic CATH Domains
1.10.1530.10 CATHdb (see all for 1s20)
Click To Show Structure

Enzyme Reaction (EC:1.1.1.130)

2,3-diketogulonate
CHEBI:57441ChEBI
+
NADH(2-)
CHEBI:57945ChEBI
+
hydron
CHEBI:15378ChEBI
→
3-dehydro-L-gulonate
CHEBI:57655ChEBI
+
NAD(1-)
CHEBI:57540ChEBI
Alternative enzyme names: 3-keto-L-gulonate dehydrogenase, 3-ketogulonate dehydrogenase, 2,3-diketo-L-gulonate reductase,

Enzyme Mechanism

Introduction

His 44 protonates the oxygen attached to C2 of the substrate. NADH is the source of a hydride, which nucleophilically attacks C2 of the substrate to give the product, and NAD+. The proposed mechanism is based on the crystal structure only.

Catalytic Residues Roles

UniProt PDB* (1s20)
His44 His44A His 44 protonates the oxygen attached to the C2 atom of the substrate. 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

overall reactant used, overall product formed, hydride transfer, bimolecular nucleophilic addition, aromatic unimolecular elimination by the conjugate base, proton transfer, inferred reaction step, native state of enzyme regenerated

References

  1. Forouhar F et al. (2004), J Biol Chem, 279, 13148-13155. A Novel NAD-binding Protein Revealed by the Crystal Structure of 2,3-Diketo-L-gulonate Reductase (YiaK). DOI:10.1074/jbc.m313580200. PMID:14718529.
  2. Yew WS et al. (2002), J Bacteriol, 184, 302-306. Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons. PMID:11741871.

Step 1. The protonated form of the His44 side chain acts as a general acid catalyst and polarises the C-2 carbonyl of the substrate. This facilitates the hydride transfer from NADH to C-2 of the substrate.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His44A proton donor

Chemical Components

overall reactant used, overall product formed, hydride transfer, ingold: bimolecular nucleophilic addition, ingold: aromatic unimolecular elimination by the conjugate base

Step 2. In an inferred reaction step His44 is reprotonated to regenerate the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
His44A proton acceptor

Chemical Components

proton transfer, inferred reaction step, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. The protonated form of the His44 side chain acts as a general acid catalyst and polarises the C-2 carbonyl of the substrate. This facilitates the hydride transfer from NADH to C-2 of the substrate.

Step 2. In an inferred reaction step His44 is reprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Ellie Wright, Gemma L. Holliday, Amelia Brasnett