Phosphoglycerate mutase (2,3-bisphosphoglycerate-independent)

 

Phosphoglycerate mutase catalyses a number of reactions, the most biologically relevant being the interconversion of glycerate-3-phosphate and glycerate-2-phosphate in the glycolysis and gluconeogenesis pathways.

 

Reference Protein and Structure

Sequence
Q9X519 UniProt (5.4.2.12) IPR005995 (Sequence Homologues) (PDB Homologues)
Biological species
Geobacillus stearothermophilus (Bacteria) Uniprot
PDB
1o98 - 1.4A CRYSTAL STRUCTURE OF PHOSPHOGLYCERATE MUTASE FROM BACILLUS STEAROTHERMOPHILUS COMPLEXED WITH 2-PHOSPHOGLYCERATE (1.4 Å) PDBe PDBsum 1o98
Catalytic CATH Domains
3.40.1450.10 CATHdb 3.40.720.10 CATHdb (see all for 1o98)
Cofactors
Water (1), Manganese(2+) (2)
Click To Show Structure

Enzyme Reaction (EC:5.4.2.12)

2-phosphonato-D-glycerate(3-)
CHEBI:58289ChEBI
→
3-phosphonato-D-glycerate(3-)
CHEBI:58272ChEBI
Alternative enzyme names: Cofactor independent phosphoglycerate mutase, 2,3-diphosphoglycerate-independent phosphoglycerate mutase, Phosphoglycerate phosphomutase, Phosphoglyceromutase, Monophosphoglycerate mutase, Monophosphoglyceromutase, GriP mutase, PGA mutase, IPGM, IPGAM, PGAM-i,

Enzyme Mechanism

Introduction

The active site contains two Mn2+ ions. Mn1 and Arg 261 coordinate the substrate; this stabilises the negative charge of the substrate and transition states, and increases the electrophilicity of the phosphorus atom. The transfer of the phosphate group between the oxygen atom on C3 and the oxygen atom on C2 on glycerate is facilitated by the hydroxyl group of Ser 62 (activated by Mn2), which attacks the phosphorus centre and causes the glycerate-phosphate bond to break in an SN2. This creates a phospho-serine intermediate. Asp 154 deprotonates the C2 hydroxyl group of the glycerate substrate, which can move in the active site so that this newly deprotonated hydroxyl can attack the phosphorus centre, and break the phospho-serine bond in another SN2 reaction. This regenerates Ser 62. A water molecule, activated by Mn1, acts as a specific acid to neutralise the C3 hydroxide group and to release the product from coordination to Mn1.

Catalytic Residues Roles

UniProt PDB* (1o98)
Arg261 Arg261A Arg 261 coordinates the phosphate group throughout the reaction, stabilising the intermediates and transition states, and increasing the electrophilicity of the phosphate group. electrostatic stabiliser
Lys336 Lys336A Deprotonates the Ser 62 to activate the thiol group along with Mn2 proton acceptor, proton donor
Asp403, His407, His462, Asp12, His445, Asp444 Asp403A, His407A, His462A, Asp12A, His445A, Asp444A Coordinate the Mn ion. metal ligand
Ser62 Ser62A Ser 62 is nucleophilic (activated by Mn2) and attacks the phosphate group of glycerate-3-phosphate. This breaks the glycerate-phosphate bond in an SN2 mechanism, and forms a phospho-enzyme intermediate. Ser 62 is regenerated when the substrate's C2 hydroxide group attacks the phospho-enzyme intermediate in an SN2 reaction. nucleofuge, nucleophile, metal ligand, proton acceptor, proton donor
Asp154 Asp154A Asp 154 deprotonates the C2 hydroxyl group of the substrate, making it nucleophilic enough to attack the phospho-enzyme intermediate. 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

decoordination from a metal ion, coordination to a metal ion, proton transfer, overall reactant used, bimolecular nucleophilic substitution, intermediate formation, intermediate terminated, overall product formed, native state of enzyme regenerated, native state of cofactor regenerated

References

  1. Jedrzejas MJ et al. (2000), EMBO J, 19, 1419-1431. Structure and mechanism of action of a novel phosphoglycerate mutase from Bacillus stearothermophilus. DOI:10.1093/emboj/19.7.1419. PMID:10747010.
  2. Nukui M et al. (2007), Biophys J, 92, 977-988. Structure and molecular mechanism of Bacillus anthracis cofactor-independent phosphoglycerate mutase: a crucial enzyme for spores and growing cells of Bacillus species. DOI:10.1529/biophysj.106.093872. PMID:17085493.

Step 1. The water molecule coordinating the first Mn ion is replaced by the ester oxygen of 2-phospho-D-glycerate.

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Catalytic Residues Roles

Residue Roles
Asp12A metal ligand
Ser62A metal ligand
Asp403A metal ligand
His407A metal ligand
Asp444A metal ligand
His445A metal ligand
His462A metal ligand
Arg261A electrostatic stabiliser

Chemical Components

decoordination from a metal ion, coordination to a metal ion

Step 2. Ser 62 is polarized by the second Mn ion. This polarization leads to Lys 336 deprotonating Ser 62, which activates the thiol group.

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Catalytic Residues Roles

Residue Roles
Ser62A metal ligand
Asp12A metal ligand
Asp403A metal ligand
His407A metal ligand
Asp444A metal ligand
His445A metal ligand
His462A metal ligand
Arg261A electrostatic stabiliser
Lys336A proton acceptor
Ser62A proton donor

Chemical Components

proton transfer

Step 3. There is nucleophilic attack from Ser 62 onto the phosphate group of 2-phospho-D-glycerate. This leads to glycerate being displaced in an SN2 reaction forming a phospho-serine intermediate.

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Catalytic Residues Roles

Residue Roles
Ser62A metal ligand
Asp12A metal ligand
Asp403A metal ligand
His407A metal ligand
Asp444A metal ligand
His445A metal ligand
His462A metal ligand
Arg261A electrostatic stabiliser
Ser62A nucleophile

Chemical Components

overall reactant used, ingold: bimolecular nucleophilic substitution, intermediate formation

Step 4. Asp 154 deprotonates the C2 hydroxyl of the glycerate, this activates the hydroxyl group.

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Catalytic Residues Roles

Residue Roles
Ser62A metal ligand
Asp12A metal ligand
Asp403A metal ligand
His407A metal ligand
Asp444A metal ligand
His445A metal ligand
His462A metal ligand
Arg261A electrostatic stabiliser
Asp154A proton acceptor

Chemical Components

proton transfer

Step 5. There is a second nucleophilic substitution reaction where the C2 oxygen attacks the phosphate group displacing Ser 62. This forms the (deprotonated) product of the reaction.

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Catalytic Residues Roles

Residue Roles
Ser62A metal ligand
Asp12A metal ligand
Asp403A metal ligand
His407A metal ligand
Asp444A metal ligand
His445A metal ligand
His462A metal ligand
Arg261A electrostatic stabiliser
Ser62A nucleofuge

Chemical Components

intermediate terminated, ingold: bimolecular nucleophilic substitution, overall product formed

Step 6. Ser 62 is reprotonated and Asp 154 is deprotonated regenerating the enzyme in its native state.

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Catalytic Residues Roles

Residue Roles
Ser62A metal ligand
Asp12A metal ligand
Asp403A metal ligand
His407A metal ligand
Asp444A metal ligand
His445A metal ligand
His462A metal ligand
Arg261A electrostatic stabiliser
Ser62A proton acceptor
Lys336A proton donor
Asp154A proton donor

Chemical Components

proton transfer, native state of enzyme regenerated

Step 7. Water displaces the ester oxygen to coordinate the first Mn ion.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Ser62A metal ligand
Asp12A metal ligand
Asp403A metal ligand
His407A metal ligand
Asp444A metal ligand
His445A metal ligand
His462A metal ligand
Arg261A electrostatic stabiliser

Chemical Components

decoordination from a metal ion, coordination to a metal ion, native state of cofactor regenerated
Download: Image, Marvin File

Step 1. The water molecule coordinating the first Mn ion is replaced by the ester oxygen of 2-phospho-D-glycerate.

Step 2. Ser 62 is polarized by the second Mn ion. This polarization leads to Lys 336 deprotonating Ser 62, which activates the thiol group.

Step 3. There is nucleophilic attack from Ser 62 onto the phosphate group of 2-phospho-D-glycerate. This leads to glycerate being displaced in an SN2 reaction forming a phospho-serine intermediate.

Step 4. Asp 154 deprotonates the C2 hydroxyl of the glycerate, this activates the hydroxyl group.

Step 5. There is a second nucleophilic substitution reaction where the C2 oxygen attacks the phosphate group displacing Ser 62. This forms the (deprotonated) product of the reaction.

Step 6. Ser 62 is reprotonated and Asp 154 is deprotonated regenerating the enzyme in its native state.

Step 7. Water displaces the ester oxygen to coordinate the first Mn ion.

Products.

Contributors

Jonathan T. W. Ng, Gemma L. Holliday, James Willey