Dihydroneopterin aldolase

 

7,8 dihydroneopterin from Staphylococcus aureus is able to catalyse the conversion of 7,8 dihydroneopterin to 6 hydroxymethyl 7,8 dihydroneopterin, an aldol cleavage reaction which also produces glycoaldehyde, a key step in the synthesis of folate, which can in turn be used for the synthesis of purines. The enzyme is an attractive target for antibiotics, as the it is found in MRSA, thus structural information can be used to design inhibitors of the enzyme.

 

Reference Protein and Structure

Sequence
P56740 UniProt (4.1.2.25, 5.1.99.8) IPR006156 (Sequence Homologues) (PDB Homologues)
Biological species
Staphylococcus aureus (Bacteria) Uniprot
PDB
2dhn - COMPLEX OF 7,8-DIHYDRONEOPTERIN ALDOLASE FROM STAPHYLOCOCCUS AUREUS WITH 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN AT 2.2 A RESOLUTION (2.2 Å) PDBe PDBsum 2dhn
Catalytic CATH Domains
3.30.1130.10 CATHdb (see all for 2dhn)
Cofactors
Water (1)
Click To Show Structure

Enzyme Reaction (EC:4.1.2.25)

7,8-dihydroneopterin
CHEBI:17001ChEBI
→
2-amino-6-(hydroxymethyl)-7,8-dihydropteridin-4-one
CHEBI:44841ChEBI
+
glycolaldehyde
CHEBI:17071ChEBI
Alternative enzyme names: 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine glycolaldehyde-lyase, 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine glycolaldehyde-lyase (2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine-forming), 7,8-dihydroneopterin aldolase, DHNA, MptD (gene name), FolB (gene name),

Enzyme Mechanism

Introduction

The reaction is an aldol cleavage reaction similar to those catalysed by aldolases. Deprotonation of the 7C OH by Lys 100, assisted by Glu 22, results in an unstable enamine intermediate which collapses to form the products glycoaldehyde and deprotonated 6 hydroxymethyl dho which picks up a proton from Lys 100 to regenerate the catalytically active form of the enzyme.

Catalytic Residues Roles

UniProt PDB* (2dhn)
Lys100 Lys100A Deprotonates the substrate thus forming the unstable enamine intermediate which collapses to release the products. Subsequently reprotonates the product to regenerate the active form of the enzyme. proton acceptor, proton donor
Glu22 Glu22A Assists in the deprotonation of the substrate by maintaining Lys 100 in the correct protonation state through electrostatic contacts with the residue. 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, bimolecular elimination, assisted tautomerisation (not keto-enol), native state of enzyme regenerated

References

  1. Hennig M et al. (1998), Nat Struct Biol, 5, 357-362. Crystal structure and reaction mechanism of 7,8-dihydroneopterin aldolase from staphylococcus aureus. DOI:10.1038/nsb0598-357. PMID:9586996.
  2. Wang Y et al. (2006), Biochemistry, 45, 15232-15239. Mechanism of dihydroneopterin aldolase: functional roles of the conserved active site glutamate and lysine residues. DOI:10.1021/bi060949j. PMID:17176045.

Step 1. Lys100 deprotonates the C7 hydroxyl, this results in the C6-C7 bond being broken and an enamine intermediate being formed along with glycoaldehyde. Water acts as a general acid assisting in the enamine formation.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Glu22A electrostatic stabiliser
Lys100A proton acceptor

Chemical Components

proton transfer, overall product formed, overall reactant used, ingold: bimolecular elimination

Step 2. The unstable enamine intermediate collapses upon protonation by Lys100 to form the product HP.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys100A proton donor

Chemical Components

proton transfer, assisted tautomerisation (not keto-enol), overall product formed, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Lys100 deprotonates the C7 hydroxyl, this results in the C6-C7 bond being broken and an enamine intermediate being formed along with glycoaldehyde. Water acts as a general acid assisting in the enamine formation.

Step 2. The unstable enamine intermediate collapses upon protonation by Lys100 to form the product HP.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, James Willey