dihydroxyacetone kinase, dha kinase, phosphoenolpyruvate carbohydrate phosphotransferase, atp-dependent dihydroxyacetone kinase, pep-dependent dha kinase, dihydroxyacetone kinase i, dhaki, dhak-2, more
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
subunit DhaL contains ADP as cofactor for phosphate double displacement from subunit DhaM to dihydroxyacetone phosphate, evolution of the binding site, conversion of a substrate binding site into a cofactor binding site, overview, complexing with the enzyme increases the thermal unfolding temperature
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
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
enzyme exists of 3 subunit DhaK, DhaM, and DhaL: DhaK contains the dihydroxyacetone phosphate binding site, DhaL contains ADP as cofactor for phosphate double displacement from DhaM to dihydroxyacetone phosphate, and DhaM provides a phospho-histidine relay between phosphoenolpyruvate and DhaL-ADP
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