2-dehydropantoate 2-reductase

 

Ketopantoate reductase (KPR), isolated from Escherichia coli, catalyses the reduction of ketopantoate by NADPH to form pantoate and NADP+. This is the second reaction in the pathway for the biosynthesis of pantothenate (vitamin B5). KPR is a member of the 6-phosphogluconate dehydrogenase superfamily. The reaction proceeds by a sequential ordered bi:bi kinetic mechanism, with NADPH binding first, followed by a conformational change and the binding of ketopantoate. After the reaction NADP+ dissociates first, followed by pantoate.

 

Reference Protein and Structure

Sequence
P0A9J4 UniProt (1.1.1.169) IPR003710 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1yon - Escherichia coli ketopantoate reductase in complex with 2-monophosphoadenosine-5'-diphosphate (1.95 Å) PDBe PDBsum 1yon
Catalytic CATH Domains
1.10.1040.10 CATHdb (see all for 1yon)
Click To Show Structure

Enzyme Reaction (EC:1.1.1.169)

NADPH(4-)
CHEBI:57783ChEBI
+
hydron
CHEBI:15378ChEBI
+
2-dehydropantoate
CHEBI:11561ChEBI
→
(R)-pantoate
CHEBI:15980ChEBI
+
NADP(3-)
CHEBI:58349ChEBI
Alternative enzyme names: 2-ketopantoate reductase, 2-ketopantoic acid reductase, 2-oxopantoate reductase, Ketopantoate reductase, Ketopantoic acid reductase, KPA reductase,

Enzyme Mechanism

Introduction

The pro-S hydride of NADPH is transferred to the si face of the C2 carbonyl of ketopantoate. The developing alkoxide is protonated by Lys176 to form pantoate. Asn98 stabilises the active conformation of Lys176 and promotes the dissociation of NADP+.

Catalytic Residues Roles

UniProt PDB* (1yon)
Lys176 Lys176A Involved in substrate binding. 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

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

References

  1. Ciulli A et al. (2007), J Biol Chem, 282, 8487-8497. Crystal Structure of Escherichia coli Ketopantoate Reductase in a Ternary Complex with NADP+ and Pantoate Bound: SUBSTRATE RECOGNITION, CONFORMATIONAL CHANGE, AND COOPERATIVITY. DOI:10.1074/jbc.m611171200. PMID:17229734.
  2. Ciulli A et al. (2007), Acta Crystallogr D Biol Crystallogr, 63, 171-178. pH-tuneable binding of 2′-phospho-ADP-ribose to ketopantoate reductase: a structural and calorimetric study. DOI:10.1107/s0907444906044465. PMID:17242510.
  3. Zheng R et al. (2000), Biochemistry, 39, 3708-3717. Kinetic and Mechanistic Analysis of theE. colipanE-Encoded Ketopantoate Reductase†. DOI:10.1021/bi992676g. PMID:10736170.
  4. Zheng R et al. (2000), Biochemistry, 39, 16244-16251. Identification of Active Site Residues inE. coliKetopantoate Reductase by Mutagenesis and Chemical Rescue†. DOI:10.1021/bi002134v. PMID:11123955.

Step 1. Initial binding of NADPH induces a conformational change that facilitates ketopantoate binding. Nucleophilic addition of the C4 pro-S hydride of NADPH to the si face of ketopantoate then occurs. The developing alkoxide is protonated by Lys176.

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Catalytic Residues Roles

Residue Roles
Lys176A proton donor

Chemical Components

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

Step 2. In an inferred reaction step Lys176 is reprotonated to regenerate the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys176A proton acceptor

Chemical Components

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

Step 1. Initial binding of NADPH induces a conformational change that facilitates ketopantoate binding. Nucleophilic addition of the C4 pro-S hydride of NADPH to the si face of ketopantoate then occurs. The developing alkoxide is protonated by Lys176.

Step 2. In an inferred reaction step Lys176 is reprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Gemma L. Holliday, Amelia Brasnett