Glucose-6-phosphate isomerase

 

Phosphoglucose isomerase (EC:5.3.1.9) (PGI) [PMID:1593646] is a dimeric enzyme that catalyses the reversible isomerisation of glucose-6-phosphate and fructose-6-phosphate. PGI is involved in different pathways: in most higher organisms it is involved in glycolysis; in mammals it is involved in gluconeogenesis; in plants in carbohydrate biosynthesis; in some bacteria it provides a gateway for fructose into the Entner-Doudouroff pathway. The multifunctional protein, PGI, is also known as neuroleukin (a neurotrophic factor that mediates the differentiation of neurons), autocrine motility factor (a tumour-secreted cytokine that regulates cell motility), differentiation and maturation mediator and myofibril-bound serine proteinase inhibitor, and has different roles inside and outside the cell. In the cytoplasm, it catalyses the second step in glycolysis, while outside the cell it serves as a nerve growth factor and cytokine [PMID:10653639].

 

Reference Protein and Structure

Sequence
Q9N1E2 UniProt (5.3.1.9) IPR001672 (Sequence Homologues) (PDB Homologues)
Biological species
Oryctolagus cuniculus (rabbit) Uniprot
PDB
1dqr - CRYSTAL STRUCTURE OF RABBIT PHOSPHOGLUCOSE ISOMERASE, A GLYCOLYTIC ENZYME THAT MOONLIGHTS AS NEUROLEUKIN, AUTOCRINE MOTILITY FACTOR, AND DIFFERENTIATION MEDIATOR (2.5 Å) PDBe PDBsum 1dqr
Catalytic CATH Domains
3.40.50.10490 CATHdb 1.10.1390.10 CATHdb (see all for 1dqr)
Click To Show Structure

Enzyme Reaction (EC:5.3.1.9)

alpha-D-glucose 6-phosphate(2-)
CHEBI:58225ChEBI
→
D-fructofuranose 6-phosphate(2-)
CHEBI:61527ChEBI
Alternative enzyme names: D-glucose-6-phosphate ketol-isomerase, Glucose phosphate isomerase, Hexose phosphate isomerase, Hexosephosphate isomerase, Oxoisomerase, Phosphoglucoisomerase, Phosphoglucose isomerase, Phosphohexoisomerase, Phosphohexomutase, Phosphohexose isomerase, Phosphosaccharomutase, Hexose monophosphate isomerase,

Enzyme Mechanism

Introduction

The proposed mechanism for sugar isomerisation involves several steps and is thought to occur via general acid/base catalysis. Since glucose 6-phosphate and fructose 6-phosphate exist predominantly in their cyclic forms, PGI is believed to catalyse first the opening of the hexose ring to yield the straight chain form of the substrates. Glucose 6-phosphate and fructose 6-phosphate then undergo isomerisation via formation of a cis-enediol intermediate with the double bond located between C-1 and C-2. The intermediate then undergoes a second keto-enol tautomerisation with reprotonation of the substrate occuring at C1. This is then followed by ring closure.

Catalytic Residues Roles

UniProt PDB* (1dqr)
Gly272 (main-N) Gly271A (main-N) Helps stabilise the transition states formed. electrostatic stabiliser
Lys211 Lys210A Lys210 supplies some positive charge to the phosphate binding site helping to bind the substrate (also helps determine substrate specificity) and also to stabilise the transition states formed. electrostatic stabiliser
Glu217 Glu216A Forms a catalytic dyad with His388; stabilises and activates the histidine to act as a general acid/base. modifies pKa
Arg273 Arg272A Arg272 in PGI may serve a function similar to that of Lys12 in triosephosphate isomerase; it sets the overall electrostatic potential at the substrate to be positive and provides stabilisation for the negative charges that develop on the enediolate-like transition states. electrostatic stabiliser
Glu358 Glu357A Acts as a general acid/base. Proposed to be the base that abstracts the proton from C2 and then returns it to C1. proton acceptor, proton donor
Lys519 Lys518A Lys518 acts as the general acid catalyst to complete the formation of the enediol intermediate. It also acts as a general base catalyst to form the ring-opened form of fructose 6-phosphate. proton acceptor, proton donor
His389 His388B Acts as a general acid/base. This residue is most likely the base that catalyses ring opening, but it has also been suggested to abstracts the proton from C2. In either case, it is activated by Glu216. 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

decyclisation, proton transfer, overall reactant used, intramolecular elimination, assisted keto-enol tautomerisation, intramolecular nucleophilic addition, native state of enzyme regenerated, cyclisation

References

  1. Jeffery CJ et al. (2001), Biochemistry, 40, 1560-1566. Crystal Structure of Rabbit Phosphoglucose Isomerase Complexed with 5-Phospho-d-Arabinonate Identifies the Role of Glu357 in Catalysis‡. DOI:10.1021/bi0018483.
  2. Lee JH et al. (2005), Protein Sci, 14, 727-734. The crystal structure of rabbit phosphoglucose isomerase complexed with D-sorbitol-6-phosphate, an analog of the open chain form of D-glucose-6-phosphate. DOI:10.1110/ps.041070205. PMID:15689508.
  3. Solomons JT et al. (2004), J Mol Biol, 342, 847-860. The crystal structure of mouse phosphoglucose isomerase at 1.6A resolution and its complex with glucose 6-phosphate reveals the catalytic mechanism of sugar ring opening. DOI:10.1016/j.jmb.2004.07.085. PMID:15342241.
  4. Arsenieva D et al. (2002), Proc Natl Acad Sci U S A, 99, 5872-5877. The crystal structure of rabbit phosphoglucose isomerase complexed with 5-phospho-D-arabinonohydroxamic acid. DOI:10.1073/pnas.052131799. PMID:11983887.
  5. Lee JH et al. (2001), Biochemistry, 40, 7799-7805. Crystal Structure of Rabbit Phosphoglucose Isomerase Complexed with Its Substrated-Fructose 6-Phosphate‡. DOI:10.1021/bi002916o.
  6. Jeffery CJ et al. (2000), Biochemistry, 39, 955-964. Crystal structure of rabbit phosphoglucose isomerase, a glycolytic enzyme that moonlights as neuroleukin, autocrine motility factor, and differentiation mediator. DOI:10.2210/pdb1dqr/pdb. PMID:10653639.
  7. Achari A et al. (1981), Philos Trans R Soc Lond B Biol Sci, 293, 145-157. Glucose-6-phosphate isomerase. PMID:6115414.

Step 1. Ring opening step. His388 abstracts a proton from substrate, breaking the C-O bond and forming the open sugar ring.

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Catalytic Residues Roles

Residue Roles
Glu216A modifies pKa
Lys210A electrostatic stabiliser
Arg272A electrostatic stabiliser
His388B proton acceptor
Lys518A proton donor

Chemical Components

decyclisation, proton transfer, overall reactant used, ingold: intramolecular elimination

Step 2. Glu357 abstracts a proton from the C2 position of the open chain form of the substrate, resulting in the cis-enediol(ate) intermediate. His398 is inferred to act as the general acid in this step due to its proximity.

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Catalytic Residues Roles

Residue Roles
Lys210A electrostatic stabiliser
Gly271A (main-N) electrostatic stabiliser
Arg272A electrostatic stabiliser
Glu216A modifies pKa
Glu357A proton acceptor

Chemical Components

assisted keto-enol tautomerisation, proton transfer

Step 3. The protonated Glu357 side chain then transfers the same proton to the C-1 position of the intermediate, yielding the open chain form of d-fructose-6-phosphate

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys210A electrostatic stabiliser
Gly271A (main-N) electrostatic stabiliser
Arg272A electrostatic stabiliser
Glu216A modifies pKa
Glu357A proton donor

Chemical Components

assisted keto-enol tautomerisation, proton transfer

Step 4. Lys518 initiates the catalytic ring closure reaction to form the final product,

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Lys210A electrostatic stabiliser
Gly271A (main-N) electrostatic stabiliser
Arg272A electrostatic stabiliser
Glu216A modifies pKa
Lys518A proton acceptor
His388B proton donor

Chemical Components

ingold: intramolecular nucleophilic addition, proton transfer, native state of enzyme regenerated, cyclisation
Download: Image, Marvin File

Step 1. Ring opening step. His388 abstracts a proton from substrate, breaking the C-O bond and forming the open sugar ring.

Step 2. Glu357 abstracts a proton from the C2 position of the open chain form of the substrate, resulting in the cis-enediol(ate) intermediate. His398 is inferred to act as the general acid in this step due to its proximity.

Step 3. The protonated Glu357 side chain then transfers the same proton to the C-1 position of the intermediate, yielding the open chain form of d-fructose-6-phosphate

Step 4. Lys518 initiates the catalytic ring closure reaction to form the final product,

Products.

Contributors

James W. Murray, Craig Porter, Gemma L. Holliday