Shikimate dehydrogenase

 

Shikimate dehydrogenase catalyses the fourth step of the shikimate pathway, an essential aromatic biosynthesis pathway in plants and microorganisms. This enzyme belongs to the shikimate dehydrogenase family, in the superfamily of NAD(P)H-dependent oxidoreductases. The shikimate pathway is an attractive target for antifungal, antiparasite and herbicidal agents, and also for research into possible biosynthesis of hydroaromatic compounds for industrial processes.

 

Reference Protein and Structure

Sequence
Q5SJF8 UniProt (1.1.1.25) IPR011342 (Sequence Homologues) (PDB Homologues)
Biological species
Thermus thermophilus HB8 (Bacteria) Uniprot
PDB
2cy0 - Crystal Structure of Shikimate 5-Dehydrogenase (AroE) from Thermus Thermophilus HB8 in complex with NADP (1.9 Å) PDBe PDBsum 2cy0
Catalytic CATH Domains
3.40.50.10860 CATHdb 3.40.50.720 CATHdb (see all for 2cy0)
Click To Show Structure

Enzyme Reaction (EC:1.1.1.25)

shikimate
CHEBI:36208ChEBI
+
NADP(3-)
CHEBI:58349ChEBI
→
3-dehydroshikimate
CHEBI:16630ChEBI
+
hydron
CHEBI:15378ChEBI
+
NADPH(4-)
CHEBI:57783ChEBI
Alternative enzyme names: 5-dehydroshikimate reductase, 5-dehydroshikimic reductase, AroE, DHS reductase, Dehydroshikimic reductase, Shikimate 5-dehydrogenase, Shikimate oxidoreductase, Shikimate:NADP(+) 5-oxidoreductase, Shikimate:NADP(+) oxidoreductase, Shikimate dehydrogenase,

Enzyme Mechanism

Introduction

Shikimate 5-dehydrogenase catalyses the reduction of 3-dehydroshikimate to shikimate using an NADH cofactor. Lys64 acts as a general base by in the initial proton abstraction from shikimate and Asp100 facilitates the hydride transfer between shikimate and NADP+.

Catalytic Residues Roles

UniProt PDB* (2cy0)
Lys64 Lys64A Acts as a general base to deprotonate the 5-hydroxyl group of shikimate. proton acceptor, proton donor
Asp100 Asp100A The negative charge of Asp100 may facilitate the proton abstraction of Lys64. Lys64 and Asp100 are coupled by a salt bridge and may act as a catalytic diad. 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, overall product formed, overall reactant used, cofactor used, aromatic bimolecular nucleophilic addition, inferred reaction step, native state of enzyme regenerated

References

  1. Benach J et al. (2003), J Biol Chem, 278, 19176-19182. The 2.3-A Crystal Structure of the Shikimate 5-Dehydrogenase Orthologue YdiB from Escherichia coli Suggests a Novel Catalytic Environment for an NAD-dependent Dehydrogenase. DOI:10.1074/jbc.m301348200. PMID:12624088.
  2. Peek J et al. (2011), Biochemistry, 50, 8616-8627. Structural and mechanistic analysis of a novel class of shikimate dehydrogenases: evidence for a conserved catalytic mechanism in the shikimate dehydrogenase family. DOI:10.1021/bi200586y. PMID:21846128.
  3. Bagautdinov B et al. (2007), J Mol Biol, 373, 424-438. Crystal structures of shikimate dehydrogenase AroE from Thermus thermophilus HB8 and its cofactor and substrate complexes: insights into the enzymatic mechanism. DOI:10.1016/j.jmb.2007.08.017. PMID:17825835.
  4. Gan J et al. (2007), Biochemistry, 46, 9513-9522. Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism. DOI:10.1021/bi602601e. PMID:17649975.
  5. Lindner HA et al. (2005), J Biol Chem, 280, 7162-7169. Site-directed mutagenesis of the active site region in the quinate/shikimate 5-dehydrogenase YdiB of Escherichia coli. DOI:10.1074/jbc.M412028200. PMID:15596430.
  6. Padyana AK et al. (2003), Structure, 11, 1005-1013. Crystal Structure of Shikimate 5-Dehydrogenase (SDH) Bound to NADP. DOI:10.1016/s0969-2126(03)00159-x. PMID:12906831.
  7. Michel G et al. (2003), J Biol Chem, 278, 19463-19472. Structures of Shikimate Dehydrogenase AroE and Its Paralog YdiB: A COMMON STRUCTURAL FRAMEWORK FOR DIFFERENT ACTIVITIES. DOI:10.1074/jbc.m300794200. PMID:12637497.
  8. Ye S et al. (2003), J Bacteriol, 185, 4144-4151. The Crystal Structure of Shikimate Dehydrogenase (AroE) Reveals a Unique NADPH Binding Mode. DOI:10.1128/jb.185.14.4144-4151.2003. PMID:12837789.

Step 1. Lys64 acts as a general base and abstracts a proton from the 5-hydroxyl group of shikimate. The hydride at C5 of shikimate is transferred to C4 of NADP+ in a bimolecular aromatic nucleophilic addition reaction, forming the product.

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Catalytic Residues Roles

Residue Roles
Asp100A electrostatic stabiliser
Lys64A proton acceptor

Chemical Components

proton transfer, overall product formed, overall reactant used, cofactor used, ingold: aromatic bimolecular nucleophilic addition

Step 2. In an inferred reaction step Lys64 is deprotonated to regenerate the native state of the enzyme.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys64A proton donor

Chemical Components

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

Step 1. Lys64 acts as a general base and abstracts a proton from the 5-hydroxyl group of shikimate. The hydride at C5 of shikimate is transferred to C4 of NADP+ in a bimolecular aromatic nucleophilic addition reaction, forming the product.

Step 2. In an inferred reaction step Lys64 is deprotonated to regenerate the native state of the enzyme.

Products.

Contributors

Gary McDowell, Gemma L. Holliday, Amelia Brasnett