Literature summary for 2.7.1.29 extracted from
Bordes, I.; Garcia-Junceda, E.; Sanchez-Moreno, I.; Castillo, R.; Moliner, V.
Computational study of the phosphoryl donor activity of dihydroxyacetone kinase from ATP to inorganic polyphosphate (2018), Int. J. Quantum Chem., 118, e25520 .
No PubMed abstract available
Protein Variants
Protein Variants |
Comment |
Organism |
E526K |
based on the use of hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, with the QM region described by semiempirical and DFT methods, the reaction mechanism of the wild-type enzyme and the most active experimentally measured mutant (Glu526Lys) with polyphosphate as phosphoryl donor is explored to elucidate the origin of the activity of this mutant. The mutation favors a more adequate position of the polyphosphate in the active site for the following step, the chemical reaction, to take place. Structure-function analysis, overview |
Citrobacter freundii |
Metals/Ions
Metals/Ions |
Comment |
Organism |
Structure |
Mg2+ |
required, the phosphate groups of the nucleotide are coordinated via two magnesium ions to the side-chain carboxyl groups of aspartates |
Citrobacter freundii |
|
Natural Substrates/ Products (Substrates)
Natural Substrates |
Organism |
Comment (Nat. Sub.) |
Natural Products |
Comment (Nat. Pro.) |
Rev. |
Reac. |
ATP + glycerone |
Citrobacter freundii |
- |
ADP + glycerone phosphate |
- |
? |
|
Organism
Organism |
UniProt |
Comment |
Textmining |
Citrobacter freundii |
P45510 |
- |
- |
Reaction
Reaction |
Comment |
Organism |
Reaction ID |
ATP + glycerone = ADP + glycerone phosphate |
reaction mechanism analysis using hybrid quantum mechanics/molecular mechanics (QM/MM). Asp-assisted mechanism for the phosphorylation reaction from I2 to PAsp, and substrate-assisted mechanism, overview |
Citrobacter freundii |
|
Substrates and Products (Substrate)
Substrates |
Comment Substrates |
Organism |
Products |
Comment (Products) |
Rev. |
Reac. |
ATP + glycerone |
- |
Citrobacter freundii |
ADP + glycerone phosphate |
- |
? |
|
Subunits
Subunits |
Comment |
Organism |
homodimer |
each subunit is formed by two domains. The dihydroxyacetone (Dha) binding site is located in the DhaK-domain while the ATP binding site is in the DhaL-domain. In the dimer, the subunits are disposed in an anti-parallel way. Therefore, the DhaK-domain of one subunit is faced with the DhaL-domain of the other subunit. The ATP binding domain is a barrel composed by eight amphipathic alpha-helix stabilized by a lipid. The phosphate groups of the nucleotide are coordinated via two magnesium ions to the side-chain carboxyl groups of aspartates. Structure-function analysis, overview |
Citrobacter freundii |
Synonyms
Synonyms |
Comment |
Organism |
DhaK |
- |
Citrobacter freundii |
dihydroxyacetone kinase |
- |
Citrobacter freundii |
General Information
General Information |
Comment |
Organism |
additional information |
analysis of the reaction mechanism of the wild-type enzyme and the most active experimentally measured mutant (Glu526Lys) with polyphosphate as phosphoryl donor by use of hybrid quantum mechanics/molecular mechanics (QM/MM) potentials, with the QM region described by semiempirical and DFT methods. The initial coordinates of the protein and the phospholipid are taken from the X-ray structure of the apoform of enzyme DHAK from Citrobacter freundii (PDB ID 1UN8). The crystal structure contains two protein chains defined as chain A and chain B. Since the full structure is symmetric, a fragment of each chain is removed obtaining a two close domain structure where the chain A fragment corresponds to the DhaL domain, and the chain B to the DhaK-domain. Missing residues of the flexible loop of the L-domain are manually added within the help of Molden program. The coordinates of Dha and magnesium cations are taken from the PDB ID 1UN9 that corresponds to the Dha/ANP form. The ATP binding domain is a barrel composed by eight amphipathic alpha-helix stabilized by a lipid. The phosphate groups of the nucleotide are coordinated via two magnesium ions to the side-chain carboxyl groups of aspartates. Structure-function analysis, overview. Construction of the B3LYP/MM optimized structure corresponding to the transition state of the phosphoryl transfer step for the substrate-assisted mechanism obtained in the wild-type enzyme, and in the E526K mutant |
Citrobacter freundii |