1,4-dihydroxy-2-naphthoyl-CoA synthase

 

Naphthoate synthase (MenB, also known as 1,4-dihydroxy-2-naphthoyl-CoA synthase) is involved in the synthesis of 1,4-dihydroxy-2-naphthoate, a branch point metabolite leading to the biosynthesis of menaquinone (vitamin K2, in bacteria), phylloquinone (vitamin K1 in plants), and many plant pigments. The coenzyme A group is subsequently removed from the product by 1,4-dihydroxy-2-naphthoyl-CoA hydrolase (EC:3.1.2.28). It is a member of the crotonase superfamily.

 

Reference Protein and Structure

Sequence
P9WNP5 UniProt (4.1.3.36) IPR010198 (Sequence Homologues) (PDB Homologues)
Biological species
Mycobacterium tuberculosis H37Rv (Bacteria) Uniprot
PDB
1q51 - Crystal Structure of Mycobacterium tuberculosis MenB in Complex with Acetoacetyl-Coenzyme A, a Key Enzyme in Vitamin K2 Biosynthesis (2.3 Å) PDBe PDBsum 1q51
Catalytic CATH Domains
1.10.12.10 CATHdb 3.90.226.10 CATHdb (see all for 1q51)
Click To Show Structure

Enzyme Reaction (EC:4.1.3.36)

hydron
CHEBI:15378ChEBI
+
4-(2-carboxyphenyl)-4-oxobutanoyl-CoA(5-)
CHEBI:57364ChEBI
→
water
CHEBI:15377ChEBI
+
1,4-dihydroxy-2-naphthoyl-CoA(4-)
CHEBI:58897ChEBI
Alternative enzyme names: 1,4-dihydroxy-2-naphthoate synthase, Dihydroxynaphthoate synthase, Dihydroxynaphthoic acid synthetase, DHNA synthetase, o-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase (cyclizing), Naphthoate synthase, MenB, o-succinylbenzoyl-CoA dihydratase (cyclizing),

Enzyme Mechanism

Introduction

The C7 carboxylate group abstracts the pro-2S proton. The resulting enolate oxyanion is stabilised in the oxyanion hole formed by the backbone amides of Gly105 and Gly161. The intramolecular proton transfer in the previous step increases the electrophilicity of the protonated carboxylate, allowing the attack of a C=C bond to the C atom of the carboxylate. The C7 tetrahedral intermediate formed is stabilised by oxyanion hole formed by the two Tyr residues. The tetrahedral oxyanion intermediate, aided by surrounding hydrogen bond network, collapses through an internal elimination producing a molecule of water. The intermediate tautomerises to produce 1,4-dihydroxy-2-napthoyl-CoA with the aid of Asp185 and Ser190. Inferred step to return the enzyme to its native state, involving reprotonation of Tyr287' by a hydronium ion

Catalytic Residues Roles

UniProt PDB* (1q51)
Tyr287 Tyr287D Tyr115A and Tyr287B play a central role in orientating the OSB C7 carboxylate group so that it can abstract the pro-2S proton. These two residues also form an oxyanion hole that stabilises the C7 tetrahedral intermediate formed during the course of the reaction. Tyr287B also acts as a general acid/base in the elimination of water. hydrogen bond acceptor, hydrogen bond donor, polar interaction, proton acceptor, proton donor, electrostatic stabiliser, steric role
Gly105 (main-N), Gly161 (main-N) Gly105A (main-N), Gly161A (main-N) The oxyanion hole formed by the backbone amides of Gly105 and Gly161 binds the carbonyl group adjacent to the CoA and stabilise the reactive intermediate and transition states formed at that position. hydrogen bond donor, electrostatic stabiliser
Tyr115 Tyr115A Tyr115A and Tyr287B play a central role in orientating the OSB C7 carboxylate group so that it can abstract the pro-2S proton. These two residues also form an oxyanion hole that stabilises the C7 tetrahedral intermediate formed during the course of the reaction. hydrogen bond donor, electrostatic stabiliser, steric role
Asp185, Ser190 Asp185A, Ser190A Although the exact role of these residues is unknown, they are thought to be essential for the tautomerisation reaction that occurs in step 4. They have been shown simply as activating here, but they could act as general acid/bases. activator
*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 reactant used, intermediate formation, intramolecular electrophilic addition, unimolecular elimination by the conjugate base, intermediate collapse, overall product formed, keto-enol tautomerisation, assisted keto-enol tautomerisation, intermediate terminated, inferred reaction step, native state of enzyme regenerated

References

  1. Li HJ et al. (2011), Biochemistry, 50, 9532-9544. Mechanism of the Intramolecular Claisen Condensation Reaction Catalyzed by MenB, a Crotonase Superfamily Member. DOI:10.1021/bi200877x. PMID:21830810.
  2. Sun Y et al. (2013), PLoS One, 8, e63095-. Structural basis of the induced-fit mechanism of 1,4-dihydroxy-2-naphthoyl coenzyme A synthase from the crotonase fold superfamily. DOI:10.1371/journal.pone.0063095. PMID:23658663.
  3. Song H et al. (2012), Sci China Chem, 55, 98-105. Characterization of 1,4-dihydroxy-2-naphthoyl-coenzyme A synthase (MenB) in phylloquinone biosynthesis of Synechocystis sp. PCC 6803. DOI:10.1007/s11426-011-4448-y.
  4. Truglio JJ et al. (2003), J Biol Chem, 278, 42352-42360. Crystal Structure of Mycobacterium tuberculosis MenB, a Key Enzyme in Vitamin K2 Biosynthesis. DOI:10.1074/jbc.m307399200. PMID:12909628.
  5. Holden HM et al. (2001), Acc Chem Res, 34, 145-157. The crotonase superfamily: divergently related enzymes that catalyze different reactions involving acyl coenzyme a thioesters. PMID:11263873.

Step 1. Tyr115 and Tyr287' play a central role in orientating the OSB C7 carboxylate group so that it can abstract the pro-2S proton. The resulting enolate oxyanion is stabilised in the oxyanion hole formed by the backbone amides of Gly105 and Gly161 [PMID:21830810].

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Catalytic Residues Roles

Residue Roles
Gly105A (main-N) electrostatic stabiliser, hydrogen bond donor
Gly161A (main-N) electrostatic stabiliser, hydrogen bond donor
Tyr115A electrostatic stabiliser, hydrogen bond donor, steric role
Tyr287D electrostatic stabiliser, hydrogen bond donor, steric role

Chemical Components

proton transfer, overall reactant used, intermediate formation

Step 2. The intramolecular proton transfer in the previous step increases the electrophilicity of the protonated carboxylate, allowing the attack of a C=C bond to the C atom of the carboxylate. The C7 tetrahedral intermediate formed is stabilised by oxyanion hole formed by the two Tyr residues [PMID:21830810].

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly105A (main-N) electrostatic stabiliser, hydrogen bond donor
Gly161A (main-N) electrostatic stabiliser, hydrogen bond donor
Tyr115A electrostatic stabiliser, hydrogen bond donor, steric role
Tyr287D electrostatic stabiliser, hydrogen bond donor, steric role

Chemical Components

ingold: intramolecular electrophilic addition, intermediate formation

Step 3. The tetrahedral oxyanion intermediate, aided by surrounding hydrogen bond network, collapses through an internal elimination producing a molecule of water

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly105A (main-N) electrostatic stabiliser, hydrogen bond donor
Gly161A (main-N) electrostatic stabiliser, hydrogen bond donor
Tyr115A electrostatic stabiliser, hydrogen bond donor
Tyr287D electrostatic stabiliser, hydrogen bond donor, proton donor

Chemical Components

ingold: unimolecular elimination by the conjugate base, proton transfer, intermediate collapse, intermediate formation, overall product formed

Step 4. The intermediate tautomerises to produce 1,4-dihydroxy-2-napthoyl-CoA with the aid of Asp185 and Ser190

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Gly105A (main-N) electrostatic stabiliser, hydrogen bond donor
Gly161A (main-N) electrostatic stabiliser, hydrogen bond donor
Tyr115A electrostatic stabiliser, hydrogen bond donor
Tyr287D polar interaction
Asp185A activator
Ser190A activator

Chemical Components

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

Step 5. Inferred step to return the enzyme to its native state, involving reprotonation of Tyr287' by a hydronium ion

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Tyr287D hydrogen bond acceptor, proton acceptor

Chemical Components

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

Step 1. Tyr115 and Tyr287' play a central role in orientating the OSB C7 carboxylate group so that it can abstract the pro-2S proton. The resulting enolate oxyanion is stabilised in the oxyanion hole formed by the backbone amides of Gly105 and Gly161 [PMID:21830810].

Step 2. The intramolecular proton transfer in the previous step increases the electrophilicity of the protonated carboxylate, allowing the attack of a C=C bond to the C atom of the carboxylate. The C7 tetrahedral intermediate formed is stabilised by oxyanion hole formed by the two Tyr residues [PMID:21830810].

Step 3. The tetrahedral oxyanion intermediate, aided by surrounding hydrogen bond network, collapses through an internal elimination producing a molecule of water

Step 4. The intermediate tautomerises to produce 1,4-dihydroxy-2-napthoyl-CoA with the aid of Asp185 and Ser190

Step 5. Inferred step to return the enzyme to its native state, involving reprotonation of Tyr287' by a hydronium ion

Products.

Contributors

Daniel E. Almonacid, Sophie T. Williams, Gemma L. Holliday, James Willey