Rhamnulose-1-phosphate aldolase

 

L-Rhamnulose-1-phosphate aldolase (RhuA) is a Class II aldolase, which infers the use of a divalent metal ion as an electron sink in the catalytic mechanism of the aldol cleavage and addition reactions. RhuA catalyses the cleavage of L-rhmnulose-1-phosphate to dihydroxyacetone phosphate and L-lactaldehyde. This enzyme also catalyses the reverse direction in making a carbon-carbon bond. This enzyme shows similarities with L-fuculose-1-phosphate aldolase (FucA) and L-Ribulose-5-phosphate 4-epimerase (RibE).

 

Reference Protein and Structure

Sequence
P32169 UniProt (4.1.2.19) IPR013447 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1gt7 - L-rhamnulose-1-phosphate aldolase from Escherichia coli (2.7 Å) PDBe PDBsum 1gt7
Catalytic CATH Domains
3.40.225.10 CATHdb (see all for 1gt7)
Cofactors
Zinc(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:4.1.2.19)

L-rhamnulose 1-phosphate(2-)
CHEBI:58313ChEBI
→
glycerone phosphate(2-)
CHEBI:57642ChEBI
+
(S)-lactaldehyde
CHEBI:18041ChEBI
Alternative enzyme names: L-rhamnulose 1-phosphate aldolase, L-rhamnulose-phosphate aldolase, Rhamnulose phosphate aldolase, L-rhamnulose-1-phosphate lactaldehyde-lyase,

Enzyme Mechanism

Introduction

The reaction of L-Rhamnulose-1-phosphate is proposed as follows. The ring form of L-rhamnulose-1-phosphate is opened by the action of Glu 171 acting as a general acid/base catalyst, by protonation of the ring oxygen. The open form is stabilised by the zinc ion. A proton is abstracted from O4 of the diolate by the general base catalysis of Glu 117 to cause the split of the C3-C4 carbon bond and formation of a C3 carbanion - this is subsequently protonated by Glu 117 in general acid catalysis, and the products L-lactealdehyde and DHAP dissociate. The reaction can also proceed in the reverse direction.

Catalytic Residues Roles

UniProt PDB* (1gt7)
His212, His143, His141 His212A, His143A, His141A Coordinate the Zn ion metal ligand
Glu117 Glu117A Acts as a general acid/base catalyst in splitting the C3-C4 bond. proton acceptor, proton donor
Glu171 Glu171B Acts as a general acid/base catalyst in opening of the ring form of L-rhamnulose-1-phosphate. 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

proton transfer, decyclisation, bimolecular elimination, overall reactant used, overall product formed, assisted keto-enol tautomerisation

References

  1. Kroemer M et al. (2003), Biochemistry, 42, 10560-10568. Structure and Catalytic Mechanism ofl-Rhamnulose-1-phosphate Aldolase†,‡. DOI:10.1021/bi0349266. PMID:12962479.

Step 1. The ring form of L-rhamnulose-1-phosphate is opened by Glu171, which acts as an acid.The resulting open form binds to the Zn ion.

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Catalytic Residues Roles

Residue Roles
His141A metal ligand
His143A metal ligand
His212A metal ligand
Glu171B proton donor

Chemical Components

proton transfer, decyclisation

Step 2. Glu117 deprotonates the C4 hydroxyl this leads to the C3-C4 bond breaking. Forming the enolate of glycerone phosphate and acetaldehyde.

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Catalytic Residues Roles

Residue Roles
His141A metal ligand
His143A metal ligand
His212A metal ligand
Glu117A proton acceptor

Chemical Components

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

Step 3. The enolate of glycerone phosphate is protonated by Glu117 in a tautomerization which leads to the formation of the product.

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Catalytic Residues Roles

Residue Roles
His141A metal ligand
His143A metal ligand
His212A metal ligand
Glu117A proton donor

Chemical Components

assisted keto-enol tautomerisation, proton transfer, overall product formed
Download: Image, Marvin File

Step 1. The ring form of L-rhamnulose-1-phosphate is opened by Glu171, which acts as an acid.The resulting open form binds to the Zn ion.

Step 2. Glu117 deprotonates the C4 hydroxyl this leads to the C3-C4 bond breaking. Forming the enolate of glycerone phosphate and acetaldehyde.

Step 3. The enolate of glycerone phosphate is protonated by Glu117 in a tautomerization which leads to the formation of the product.

Products.

Contributors

Gary McDowell, Craig Porter, Gemma L. Holliday, James Willey