Ribose-5-phosphate isomerase

 

Ribose-5-phosphate isomerase is able to catalyse the interconversion of Ribose-5-phosphate and Ribulose-5-phosphate, an isomerisation reaction involving the open chain forms of the two sugars, important in the pentose phosphate pathway. In Escherichia coli there are two forms of the enzyme, which although they catalyse the same reaction, have entirely different mechanisms and catalytic residues. The less common Escherichia coli RpiB is described here.

 

Reference Protein and Structure

Sequence
P37351 UniProt (5.3.1.6) IPR004785 (Sequence Homologues) (PDB Homologues)
Biological species
Escherichia coli K-12 (Bacteria) Uniprot
PDB
1nn4 - Structural Genomics, RpiB/AlsB (2.2 Å) PDBe PDBsum 1nn4
Catalytic CATH Domains
3.40.1400.10 CATHdb (see all for 1nn4)
Click To Show Structure

Enzyme Reaction (EC:5.3.1.6)

aldehydo-D-ribose 5-phosphate(2-)
CHEBI:58273ChEBI
→
D-ribulose 5-phosphate(2-)
CHEBI:58121ChEBI
Alternative enzyme names: 5-phosphoribose isomerase, D-ribose 5-phosphate isomerase, D-ribose-5-phosphate ketol-isomerase, Phosphopentosisomerase, Phosphoriboisomerase, Ribose phosphate isomerase, Ribose 5-phosphate epimerase, Phosphopentoseisomerase,

Enzyme Mechanism

Introduction

The overall mechanism of the reaction is through concerted acid-base catalysis, similar to that employed by Triose Phosphate Isomerase. Initial deprotonation of the C2 atom of Ribose-5-phosphate by the catalytic base Cys 66 primed by Asp 9 leads to the formation of an enediolate intermediate. Protons are shuttled via Thr68 leaving the C1 oxygen protonated and the C2 oxygen deprotonated. The endiolate then tautomerises forming the product-D-ribulose 5-phosphate.

Catalytic Residues Roles

UniProt PDB* (1nn4)
Thr68 Thr68(81)A Acts as a proton relay transferring a proton from the C2 hydroxyl to the C1 proton relay, proton acceptor, proton donor
His99 His99(112)D Acts as a general acid leading to ring opening. proton donor
His134 His134(147)D Acts as a general base leading to ring opening. proton acceptor
Asp9 Asp9(22)A Activates Cys66 proton acceptor, proton donor
Cys66 Cys66(79)A Acts as the general base in the abstraction of a proton from Ribose-5-phosphate, then protonates the intermediate to facilitate its collapse. 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

proton transfer, decyclisation, assisted keto-enol tautomerisation, overall reactant used, overall product formed, native state of enzyme regenerated

References

  1. Zhang RG et al. (2003), J Mol Biol, 332, 1083-1094. The 2.2Å Resolution Structure of RpiB/AlsB from Escherichia coli Illustrates a New Approach to the Ribose-5-phosphate Isomerase Reaction. DOI:10.1016/j.jmb.2003.08.009. PMID:14499611.
  2. Roos AK et al. (2005), J Biol Chem, 280, 6416-6422. Competitive inhibitors of Mycobacterium tuberculosis ribose-5-phosphate isomerase B reveal new information about the reaction mechanism. DOI:10.1074/jbc.M412018200. PMID:15590681.

Step 1. Isomerization begins with the furanose ring being opened. His 134 accepts a proton from the carbon 1 hydroxyl oxygen and His 99 donates a proton to the ring oxygen. This causes the bond between carbon 1 and the ring oxygen to break.

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Catalytic Residues Roles

Residue Roles
His134(147)D proton acceptor
His99(112)D proton donor

Chemical Components

proton transfer, decyclisation

Step 2. Asp9 deprotonates Cys 66, activating the thiol group.

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Catalytic Residues Roles

Residue Roles
Asp9(22)A proton acceptor
Cys66(79)A proton donor

Chemical Components

proton transfer

Step 3. The activated thiol group of Cys66 deprotonates the aldehydo-D-ribose 5-phosphate at carbon 2. This leads to tautomerisation forming an enediol intermediate.

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Catalytic Residues Roles

Residue Roles
Cys66(79)A proton acceptor

Chemical Components

assisted keto-enol tautomerisation, proton transfer, overall reactant used

Step 4. Thr68 acts as a proton relay, leaving the hydroxyl oxygen on carbon 2 deprotonated.

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Catalytic Residues Roles

Residue Roles
Thr68(81)A proton relay
Thr68(81)A proton donor, proton acceptor

Chemical Components

proton transfer

Step 5. The enediol intermediate accepts a proton from Cys66. This leads to a second tautomerisation reaction forming the product- D-ribulose 5-phosphate.

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Catalytic Residues Roles

Residue Roles
Cys66(79)A proton donor

Chemical Components

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

Step 6. Cys66 deprotonates Asp9, restoring these residues to their original states.

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Catalytic Residues Roles

Residue Roles
Asp9(22)A proton donor
Cys66(79)A proton acceptor

Chemical Components

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

Step 1. Isomerization begins with the furanose ring being opened. His 134 accepts a proton from the carbon 1 hydroxyl oxygen and His 99 donates a proton to the ring oxygen. This causes the bond between carbon 1 and the ring oxygen to break.

Step 2. Asp9 deprotonates Cys 66, activating the thiol group.

Step 3. The activated thiol group of Cys66 deprotonates the aldehydo-D-ribose 5-phosphate at carbon 2. This leads to tautomerisation forming an enediol intermediate.

Step 4. Thr68 acts as a proton relay, leaving the hydroxyl oxygen on carbon 2 deprotonated.

Step 5. The enediol intermediate accepts a proton from Cys66. This leads to a second tautomerisation reaction forming the product- D-ribulose 5-phosphate.

Step 6. Cys66 deprotonates Asp9, restoring these residues to their original states.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, James Willey