Acetate kinase

 

Acetate kinase is a key enzyme for many methanogenic bacteria as it is able to catalyse the interconversion of acetate and acetyl phosphate using the removal of a phosphate from ATP. Structural analysis of the enzyme from Methanosarcina thermophila, an Archaea, shows that it is a member of the sugar kinase superfamily which includes hexokinase, and geochemical studies suggest that it is most likely to be the urkinase- the ancestor of all of the members of the superfamily.

 

Reference Protein and Structure

Sequence
P38502 UniProt (2.7.2.1) IPR004372 (Sequence Homologues) (PDB Homologues)
Biological species
Methanosarcina thermophila (Archaea) Uniprot
PDB
1g99 - AN ANCIENT ENZYME: ACETATE KINASE FROM METHANOSARCINA THERMOPHILA (2.5 Å) PDBe PDBsum 1g99
Catalytic CATH Domains
3.30.420.40 CATHdb (see all for 1g99)
Cofactors
Magnesium(2+) (1)
Click To Show Structure

Enzyme Reaction (EC:2.7.2.1)

ATP(4-)
CHEBI:30616ChEBI
+
acetate
CHEBI:30089ChEBI
→
acetyl phosphate(2-)
CHEBI:22191ChEBI
+
ADP(3-)
CHEBI:456216ChEBI
Alternative enzyme names: Acetokinase, AckA, AK, Acetic kinase, Acetate kinase (phosphorylating),

Enzyme Mechanism

Introduction

The proposed mechanism is an in-line single displacement reaction where the acetate acts as the nucleophile to attack the gamma phosphate of ATP, resulting in acetyl phosphate and ADP. For this reaction to take place, a magnesium ion, His180, Arg241 and Arg91 are important in stabilising the reaction transition state.

Catalytic Residues Roles

UniProt PDB* (1g99)
Asn7 Asn7A Coordinates to the magnesium ion which in turn stabilises the transition state in the reaction. metal ligand
Glu384 Glu384A Coordinates to the magnesium ion which in turn helps stabilise the transition state in the reaction. metal ligand
His180 His180A Coordinates to the equatorial oxygens on ATP to help stabilise the transition state. electrostatic stabiliser, polar interaction
Arg91 Arg91A Contacts alpha phosphate of ATP thus stabilises the phosphate transition state through electrostatic interactions. It also has been proposed to help position acetate for nucleophilic attack in the reaction. electrostatic stabiliser, polar interaction
Arg241 Arg241A Contacts alpha phosphate of ATP helping stabilise the transition state. electrostatic stabiliser, polar interaction
*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 substitution, overall product formed, overall reactant used

References

  1. Gorrell A et al. (2005), J Biol Chem, 280, 10731-10742. Structural and kinetic analyses of arginine residues in the active site of the acetate kinase from Methanosarcina thermophila. DOI:10.1074/jbc.M412118200. PMID:15647264.
  2. Buss KA et al. (2001), J Bacteriol, 183, 680-686. Urkinase: Structure of Acetate Kinase, a Member of the ASKHA Superfamily of Phosphotransferases. DOI:10.1128/jb.183.2.680-686.2001. PMID:11133963.
  3. Miles RD et al. (2001), J Biol Chem, 276, 45059-45064. Site-directed Mutational Analysis of Active Site Residues in the Acetate Kinase from Methanosarcina thermophila. DOI:10.1074/jbc.m108355200. PMID:11562377.

Step 1. Acetate's carboxyl group acts as a nucleophile and attacks and displaces the gamma-phosphate on ATP via a trigonal bypyramidal transition state.

Download: Image, Marvin File

Catalytic Residues Roles

Residue Roles
Arg91A electrostatic stabiliser
Arg241A electrostatic stabiliser
Asn7A metal ligand
Glu384A metal ligand
His180A electrostatic stabiliser
Arg91A polar interaction
His180A polar interaction
Arg241A polar interaction

Chemical Components

ingold: bimolecular nucleophilic substitution, overall product formed, overall reactant used
Download: Image, Marvin File

Step 1. Acetate's carboxyl group acts as a nucleophile and attacks and displaces the gamma-phosphate on ATP via a trigonal bypyramidal transition state.

Products.

Contributors

Peter Sarkies, Gemma L. Holliday, Morwenna Hall