Isochorismate synthase (menaquinone-specific)

 

Isochorismate synthase (MenF) catalyses the conversion of chorismate to isochorismate, the first step in the biosynthesis of both the respiratory chain component menaquinone (MK, vitamin K2) and phylloquinone (vitamin K1). This entry represents the isoform in bacteria that is mainly channelled into menaquinone synthesis.

 

Reference Protein and Structure

Sequence
P38051 UniProt (5.4.4.2) IPR034681 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
2eua - Structure and Mechanism of MenF, the Menaquinone-Specific Isochorismate Synthase from Escherichia Coli (2.5 Å) PDBe PDBsum 2eua
Catalytic CATH Domains
3.60.120.10 CATHdb (see all for 2eua)
Cofactors
Magnesium(2+) (1), Water (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:5.4.4.2)

chorismate(2-)
CHEBI:29748ChEBI
→
isochorismate(2-)
CHEBI:29780ChEBI
Alternative enzyme names: Isochorismate synthetase, Isochorismate mutase, MenF,

Enzyme Mechanism

Introduction

The catalytic base, Lys190, is position to activate water towards nucleophilic attack at the C6 position, initiating rearrangement of the ring conjugation, and eliminating water from the C4 position. It is inferred that the active site is regenerated by the transmission of a proton between the catalytic acid Glu240 and the catalytic base Lys190.

Catalytic Residues Roles

UniProt PDB* (2eua)
Glu240 Glu240A Acts as a general acid/base. Glu240 donates a proton to the leaving group water in the first step of the reaction. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, activator
Lys190 Lys190A Acts as a general acid/base. Lys190 deprotonates the catalyic water in the first step of the reaction. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, activator
Glu284, Glu416 Glu284A, Glu416A Forms part of the magnesium binding site. attractive charge-charge interaction, metal ligand, electrostatic stabiliser
Lys420 Lys420A Helps stabilise the transition state. attractive charge-charge interaction, 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

isomerisation reaction (not covered by named reactions), proton transfer, overall reactant used, overall product formed, rate-determining step, native state of enzyme regenerated, proton relay, inferred reaction step

References

  1. Kolappan S et al. (2007), Biochemistry, 46, 946-953. Lysine 190 Is the Catalytic Base in MenF, the Menaquinone-Specific Isochorismate Synthase fromEscherichia coli:  Implications for an Enzyme Family†. DOI:10.1021/bi0608515. PMID:17240978.
  2. Meneely KM et al. (2013), Arch Biochem Biophys, 538, 49-56. Lysine221 is the general base residue of the isochorismate synthase from Pseudomonas aeruginosa (PchA) in a reaction that is diffusion limited. DOI:10.1016/j.abb.2013.07.026. PMID:23942051.
  3. Sridharan S et al. (2010), J Mol Biol, 397, 290-300. Crystal Structure of Escherichia coli Enterobactin-specific Isochorismate Synthase (EntC) Bound to its Reaction Product Isochorismate: Implications for the Enzyme Mechanism and Differential Activity of Chorismate-utilizing Enzymes. DOI:10.1016/j.jmb.2010.01.019. PMID:20079748.

Step 1. The catalytic base, Lys190, is position to activate water towards nucleophilic attack at the C6 position, initiating rearrangement of the ring conjugation, and eliminating water from the C4 position.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys420A attractive charge-charge interaction, electrostatic stabiliser
Glu416A attractive charge-charge interaction, electrostatic stabiliser, metal ligand
Lys190A activator, hydrogen bond acceptor
Glu284A attractive charge-charge interaction, electrostatic stabiliser, metal ligand
Glu240A activator, hydrogen bond donor
Lys190A proton acceptor
Glu240A proton donor

Chemical Components

isomerisation reaction (not covered by named reactions), proton transfer, overall reactant used, overall product formed, rate-determining step

Step 2. It is inferred that the active site is regenerated by the transmission of a proton between the catalytic acid Glu240 and the catalytic base Lys190.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu416A attractive charge-charge interaction, metal ligand
Glu284A attractive charge-charge interaction, metal ligand, electrostatic stabiliser
Lys190A activator, hydrogen bond donor
Glu240A activator, hydrogen bond acceptor
Lys190A proton donor
Glu240A proton acceptor

Chemical Components

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

Step 1. The catalytic base, Lys190, is position to activate water towards nucleophilic attack at the C6 position, initiating rearrangement of the ring conjugation, and eliminating water from the C4 position.

Step 2. It is inferred that the active site is regenerated by the transmission of a proton between the catalytic acid Glu240 and the catalytic base Lys190.

Products.

Contributors

Sophie T. Williams, Gemma L. Holliday, James Willey