Deoxyribose-phosphate aldolase

 

The class I aldolase Deoxyribose-5-phosphate aldolase from Escherichia coli is able to catalyse the formation of DRP from acetaldehyde and glyceraldehyde-3-phosphate. As such is it a rare form of class I aldolase as it is able to catalyse the condensation between two aldehydes rather than an aldehyde and a ketone.

 

Reference Protein and Structure

Sequence
P0A6L0 UniProt (4.1.2.4) IPR023649 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1p1x - Comparison of class I aldolase binding site architecture based on the crystal structure of 2-deoxyribose-5-phosphate aldolase determined at 0.99 Angstrom resolution (0.99 Å) PDBe PDBsum 1p1x
Catalytic CATH Domains
3.20.20.70 CATHdb (see all for 1p1x)
Click To Show Structure

Enzyme Reaction (EC:4.1.2.4)

acetaldehyde
CHEBI:15343ChEBI
+
D-glyceraldehyde 3-phosphate(2-)
CHEBI:59776ChEBI
→
2-deoxy-D-ribose 5-phosphate(2-)
CHEBI:57651ChEBI
Alternative enzyme names: 2-deoxyribose-5-phosphate aldolase, Deoxyriboaldolase, Deoxyribose-5-phosphate aldolase, Phosphodeoxyriboaldolase, 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase,

Enzyme Mechanism

Introduction

The reaction proceeds via initial nucleophilic attack by Lys 167 on acetaldehyde to form a Schiff base intermediate; deprotonation of the Lys 167 by Asp 102 facilitates this. Subsequent deprotonation of the C2 of the acetaldehyde by a Lys 201 activated water molecule (Wat29) results in the production of a nucleophilic carbon centre which attacks the G3P molecule to form the linear form of the product, DRP.

Catalytic Residues Roles

UniProt PDB* (1p1x)
Asp102 Asp102(103)A Activates Lys 167 towards nucleophilic attack so that Schiff base intermediate can be formed. Also acts to protonate and deprotonate the Lys 167 in order to allow collapse of the Schiff base intermediate. Furthermore, activates water as part of proton relay system with Lys 201. proton relay, increase nucleophilicity, proton acceptor, proton donor
Lys167 Lys167(168)A Attacks electrophilic carbon centre to form Schiff base intermediate. covalently attached, nucleofuge, nucleophile, proton acceptor, proton donor, electron pair acceptor, electron pair donor
Lys201 Lys201(202)A Activates water to allow it to act as a general acid base for deprotonation at C2 of the Schiff base intermediate. Also activates Lys 167 towards nucleophilic attack. proton relay, increase nucleophilicity, proton acceptor, 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

bimolecular nucleophilic addition, intermediate formation, proton transfer, enzyme-substrate complex formation, overall reactant used, intramolecular elimination, schiff base formed, assisted tautomerisation (not keto-enol), aldol addition, intermediate terminated, overall product formed, enzyme-substrate complex cleavage, native state of enzyme regenerated

References

  1. Heine A et al. (2001), Science, 294, 369-374. Observation of Covalent Intermediates in an Enzyme Mechanism at Atomic Resolution. DOI:10.1126/science.1063601. PMID:11598300.

Step 1. Asp102 deprotonates Lys167, this activates the amine group for nucleophilic attack on the carbonyl carbon of acetaldehyde, forming a tetrahedral intermediate. The carbonyl oxygen is protonated by Lys201 via a water molecule .

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Catalytic Residues Roles

Residue Roles
Lys167(168)A covalently attached
Asp102(103)A increase nucleophilicity, proton acceptor
Lys167(168)A proton donor
Lys201(202)A proton donor
Lys167(168)A nucleophile

Chemical Components

ingold: bimolecular nucleophilic addition, intermediate formation, proton transfer, enzyme-substrate complex formation, overall reactant used

Step 2. Water is eliminated and a Schiff base intermediate is formed. This elimination is aided by general acid/base catalysis from Asp102 and Lys201.

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Catalytic Residues Roles

Residue Roles
Lys167(168)A covalently attached, electron pair donor
Lys201(202)A proton donor
Lys167(168)A proton donor
Asp102(103)A proton acceptor

Chemical Components

proton transfer, ingold: intramolecular elimination, schiff base formed

Step 3. The schiff base tautomerizes via acid/base catalysis to form a nucleophilic C=C bond.

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Catalytic Residues Roles

Residue Roles
Lys167(168)A covalently attached
Lys201(202)A proton acceptor
Lys167(168)A proton acceptor, electron pair acceptor
Asp102(103)A proton donor

Chemical Components

proton transfer, assisted tautomerisation (not keto-enol)

Step 4. The C=C bond performs a nucleophilic attack upon the carbonyl carbon of the glyceraldehyde 3-phosphate in an aldol addition. Which is again assisted by acid/base catalysis.

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Catalytic Residues Roles

Residue Roles
Lys167(168)A covalently attached
Asp102(103)A proton acceptor
Lys167(168)A proton donor
Lys201(202)A proton donor
Lys167(168)A electron pair donor

Chemical Components

aldol addition, proton transfer, schiff base formed

Step 5. A hydrolytic water performs a nucleophilic attack upon the the schiff base, forming a tetrahedral intermediate. The water is activated by deprotonation from Lys201.

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Catalytic Residues Roles

Residue Roles
Lys201(202)A increase nucleophilicity
Lys167(168)A covalently attached, proton acceptor
Asp102(103)A proton acceptor
Lys201(202)A proton donor
Asp102(103)A proton donor, proton relay
Lys201(202)A proton relay
Lys167(168)A electron pair acceptor
Lys201(202)A proton acceptor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer

Step 6. Lys167 is cleaved from the substrate forming the product and regenerating the enzyme in its native state.

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Catalytic Residues Roles

Residue Roles
Asp102(103)A proton donor
Lys167(168)A nucleofuge, proton acceptor
Lys201(202)A proton acceptor

Chemical Components

ingold: intramolecular elimination, intermediate terminated, overall product formed, enzyme-substrate complex cleavage, proton transfer, native state of enzyme regenerated
Download: Image, Marvin File

Step 1. Asp102 deprotonates Lys167, this activates the amine group for nucleophilic attack on the carbonyl carbon of acetaldehyde, forming a tetrahedral intermediate. The carbonyl oxygen is protonated by Lys201 via a water molecule .

Step 2. Water is eliminated and a Schiff base intermediate is formed. This elimination is aided by general acid/base catalysis from Asp102 and Lys201.

Step 3. The schiff base tautomerizes via acid/base catalysis to form a nucleophilic C=C bond.

Step 4. The C=C bond performs a nucleophilic attack upon the carbonyl carbon of the glyceraldehyde 3-phosphate in an aldol addition. Which is again assisted by acid/base catalysis.

Step 5. A hydrolytic water performs a nucleophilic attack upon the the schiff base, forming a tetrahedral intermediate. The water is activated by deprotonation from Lys201.

Step 6. Lys167 is cleaved from the substrate forming the product and regenerating the enzyme in its native state.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, James Willey