L-ribulose-5-phosphate 4-epimerase

 

L-ribulose-5-phosphate-4-epimerase catalyses the interconversion of L-ribulose 5-phosphate(L-Ru5P) and D-xylulose 5-phosphate(D-Xu5P). It belongs to a superfamily of epimerases/aldolases that catalyse carbon-carbon bond cleavage reactions via a metal stabilised enolate intermediate. The conversion from L-Ru5P to D-Xu5P allows bacteria to utilise arabinose as an energy source by converting it into an intermediate in the pentose phosphate pathway(D-Xu5P).

 

Reference Protein and Structure

Sequence
P08203 UniProt (5.1.3.4) IPR033748 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1jdi - CRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE (2.4 Å) PDBe PDBsum 1jdi
Catalytic CATH Domains
3.40.225.10 CATHdb (see all for 1jdi)
Cofactors
Zinc(2+) (1) Metal MACiE
Click To Show Structure

Enzyme Reaction (EC:5.1.3.4)

L-ribulose 5-phosphate(2-)
CHEBI:58226ChEBI
→
D-xylulose 5-phosphate(2-)
CHEBI:57737ChEBI
Alternative enzyme names: Phosphoribulose isomerase, Ribulose phosphate 4-epimerase, L-ribulose-phosphate 4-epimerase, L-ribulose 5-phosphate 4-epimerase, AraD, L-ru5P,

Enzyme Mechanism

Introduction

The mechanism involves the initial retroaldol cleavage between C3 and C4 of the substrate after the deprotonation of the C4-OH group by a base. The cleavage generates glycolaldehyde phosphate and metal -bound enolate of dihydroxyactone as intermediates. A subsequent aldol addition of the same face of the enolate to the opposite face of the aldehyde generates the epimeric product. Tyr229 acts as the base for the deprotonation of L-Ru5P while Asp120 acts as the acid to protonate the product to complete the epimerisation. In the reverse reaction, Asp acts as the base to deprotonate D-Xu5P and Tyr229 the acid. Zn2+ acts as an electrophilic catalyst by coordinating to the ketone oxygen at C2 to promote enolate formation.

Catalytic Residues Roles

UniProt PDB* (1jdi)
His95, His97, His171 His95A, His97A, His171A Binds the Zn ion metal ligand
Tyr229 TyrNone(229)A Plays a role as acid/base in catalysis. In the conversion from L-Ru5P to D-Xu5P, it acts as a base to deprotonate the substrate, L-Ru5P. In the reverse reaction, it acts as an acid to protonate the product, L-Ru5P. hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
Asp120 Asp120A(AC) In the conversion from D-Xu5P to L-Ru5P, it acts as a base to deprotonate the substrate, D-Xu5P. In the reverse reaction, it acts as an acid to protonate the product, D-Xu5P. hydrogen bond acceptor, hydrogen bond donor, 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 elimination, intermediate formation, overall reactant used, bimolecular nucleophilic addition, proton transfer, intermediate terminated, overall product formed, native state of enzyme regenerated, inferred reaction step

References

  1. Samuel J et al. (2001), Biochemistry, 40, 14772-14780. Catalysis and Binding inl-Ribulose-5-Phosphate 4-Epimerase:  A Comparison withl-Fuculose-1-Phosphate Aldolase†,‡. DOI:10.1021/bi011252v. PMID:11732896.
  2. Luo Y et al. (2001), Biochemistry, 40, 14763-14771. The Structure ofl-Ribulose-5-Phosphate 4-Epimerase:  An Aldolase-like Platform for Epimerization†,‡. DOI:10.1021/bi0112513. PMID:11732895.
  3. Lee LV et al. (2000), Biochemistry, 39, 4821-4830. Role of Metal Ions in the Reaction Catalyzed byl-Ribulose-5-phosphate 4-Epimerase†. DOI:10.1021/bi9928952. PMID:10769139.

Step 1. Initial retroaldol cleavage between C3 and C4 of the substrate after the deprotonation of the C4-OH group by Tyr229. After the initial cleavege, the glycolaldehyde phosphate intermediate rotates in the active site in order to present the opposite face to the enolate intermediate.

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Catalytic Residues Roles

Residue Roles
Asp120A(AC) hydrogen bond donor
TyrNone(229)A hydrogen bond acceptor
His95A metal ligand
His97A metal ligand
His171A metal ligand
TyrNone(229)A proton acceptor

Chemical Components

ingold: bimolecular elimination, intermediate formation, overall reactant used

Step 2. Aldol addition of the same face of the enolate intermediate to the opposite face of the glycolaldehyde phosphate intermediate

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp120A(AC) hydrogen bond donor
TyrNone(229)A hydrogen bond donor
His95A metal ligand
His97A metal ligand
His171A metal ligand
Asp120A(AC) proton donor

Chemical Components

ingold: bimolecular nucleophilic addition, proton transfer, intermediate terminated, overall product formed

Step 3. Inferred return step. Asp120 deprotonates Tyr229.)ReactiveCentres=(O,H,O

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Asp120A(AC) hydrogen bond acceptor
TyrNone(229)A hydrogen bond donor
His95A metal ligand
His97A metal ligand
His171A metal ligand
Asp120A(AC) proton acceptor
TyrNone(229)A proton donor

Chemical Components

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

Step 1. Initial retroaldol cleavage between C3 and C4 of the substrate after the deprotonation of the C4-OH group by Tyr229. After the initial cleavege, the glycolaldehyde phosphate intermediate rotates in the active site in order to present the opposite face to the enolate intermediate.

Step 2. Aldol addition of the same face of the enolate intermediate to the opposite face of the glycolaldehyde phosphate intermediate

Step 3. Inferred return step. Asp120 deprotonates Tyr229.)ReactiveCentres=(O,H,O

Products.

Contributors

Gemma L. Holliday, Mei Leung, James Willey