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Information on EC 2.7.1.29 - glycerone kinase and Organism(s) Citrobacter freundii and UniProt Accession P45510

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Citrobacter freundii
UNIPROT: P45510 not found.
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The taxonomic range for the selected organisms is: Citrobacter freundii
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
dihydroxyacetone kinase, dha kinase, phosphoenolpyruvate carbohydrate phosphotransferase, atp-dependent dihydroxyacetone kinase, pep-dependent dha kinase, dihydroxyacetone kinase i, dhaki, dhak-2, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dihydroxyacetone kinase
-
acetol kinase
-
-
-
-
DHA kinase
dihydroxyacetone kinase
glycerone kinase
-
-
-
-
kinase, acetol (phosphorylating)
-
-
-
-
additional information
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
ATP + glycerone = ADP + glycerone phosphate
show the reaction diagram
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
ATP + glycerone = ADP + glycerone phosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phospho group transfer
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:glycerone phosphotransferase
-
CAS REGISTRY NUMBER
COMMENTARY hide
9027-47-8
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + glycerone
ADP + glycerone phosphate
show the reaction diagram
-
-
-
?
ATP + dihydroxyacetone
ADP + dihydroxyacetone phosphate
show the reaction diagram
ATP + DL-glyceraldehyde
ADP + DL-glyceraldehyde 3-phosphate
show the reaction diagram
-
D,L-glyceraldehyde binds strongly to the enzyme, slow product release
-
-
?
ATP + glycerone
ADP + glycerone phosphate
show the reaction diagram
-
-
i.e. dihydroxyacetone phosphate
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + glycerone
ADP + glycerone phosphate
show the reaction diagram
-
-
-
?
ATP + dihydroxyacetone
ADP + dihydroxyacetone phosphate
show the reaction diagram
-
-
-
?
ATP + glycerone
ADP + glycerone phosphate
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ADP
-
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
ATP
-
dependent on
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mg2+
required, the phosphate groups of the nucleotide are coordinated via two magnesium ions to the side-chain carboxyl groups of aspartates
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ADP
-
competitive to ATP, noncompetitive to D,L-glyceraldehyde
chloro-3-hydroxyacetone
-
binds to the active site
D,L-glyceraldehyde
-
competitive
additional information
-
glycerol, hydroxyacetone, hydroxypuruvic acid, and methylglyoxal are no inhibitors
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00035 - 0.1
ATP
0.18
D,L-glyceraldehyde
-
pH 7.5, 30°C
0.00122
dihydroxyacetone
-
pH and temperature not specified in the publication
0.005
glycerone phosphate
-
or below, pH 7.5, 30°C
additional information
additional information
-
substrate binding constants and reaction kinetics, overview
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
24.02
ATP
at pH 8.0 and 37°C
5.17
D,L-glyceraldehyde
-
pH 7.5, 30°C
24.13
dihydroxyacetone
-
pH and temperature not specified in the publication
17.5
glycerone phosphate
-
pH 7.5, 30°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
69
ATP
at pH 8.0 and 37°C
19800
dihydroxyacetone
-
pH and temperature not specified in the publication
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.14
ADP
-
pH 7.5, 30°C
0.6
D,L-glyceraldehyde
-
pH 7.5, 30°C
additional information
additional information
-
inhibition kinetics
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
phosphotransferase assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
DHAK_CITFR
552
0
57940
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
63000
2 * 63000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
homodimer
2 * 63000, SDS-PAGE
trimer
-
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
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
crystal structure of enzyme complex with an ATP analogue and dihydroxyacetone at 2.5 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
E526K
the mutant shows activity with polyphosphate
K382A
the mutant shows activity with polyphosphate
K514A
the mutant shows activity with polyphosphate
R207B
the mutant shows activity with polyphosphate
R475A
the mutant shows activity with polyphosphate
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40
-
unfolding temperature for the apo-enzyme
48.7
-
the melting temperature is 48.7°C
65
-
unfolding temperature for the ADP-bound enzyme
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
enzyme-D,L-glyceraldehyde complex is resistant to SDS
-
not affected by 2 M glycerol
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni+2/IDA agarose column chromatography and Superdex 75 gel filtration
-
nickel-iminodiacetic acid agarose column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
phylogenetic analysis
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Siebold, C.; Arnold, I.; Garcia-Alles, L.F.; Baumann, U.; Erni, B.
Crystal structure of the Citrobacter freundii dihydroxyacetone kinase reveals an eight-stranded alpha -helical barrel ATP-binding domain
J. Biol. Chem.
278
48236-48244
2003
Citrobacter freundii (P45510), Citrobacter freundii
Manually annotated by BRENDA team
Garcia-Alles, L.F.; Siebold, C.; Nyffeler, T.L.; Flukiger-Bruhwiler, K.; Schneider, P.; Burgi, H.B.; Baumann, U.; Erni, B.
Phosphoenolpyruvate- and ATP-dependent dihydroxyacetone kinases: covalent substrate-binding and kinetic mechanism
Biochemistry
43
13037-13045
2004
Citrobacter freundii, Escherichia coli (P37349), Escherichia coli
Manually annotated by BRENDA team
Bachler, C.; Flukiger-Bruhwiler, K.; Schneider, P.; Bahler, P.; Erni, B.
From ATP as substrate to ADP as coenzyme: functional evolution of the nucleotide binding subunit of dihydroxyacetone kinases
J. Biol. Chem.
280
18321-18325
2005
Citrobacter freundii, Escherichia coli
Manually annotated by BRENDA team
Iturrate, L.; Sanchez-Moreno, I.; Oroz-Guinea, I.; Perez-Gil, J.; Garcia-Junceda, E.
Preparation and characterization of a bifunctional aldolase/kinase enzyme: a more efficient biocatalyst for C-C bond formation
Chemistry
16
4018-4030
2010
Citrobacter freundii, Citrobacter freundii CECT 4626
Manually annotated by BRENDA team
Sanchez-Moreno, I.; Bordes, I.; Castillo, R.; Ruiz-Pernia, J.J.; Moliner, V.; Garcia-Junceda, E.
Tuning the phosphoryl donor specificity of dihydroxyacetone kinase from ATP to inorganic polyphosphate. An insight from computational studies
Int. J. Mol. Sci.
16
27835-27849
2015
Citrobacter freundii (Q1KLC3), Citrobacter freundii, Citrobacter freundii CECT 4626 (Q1KLC3)
Manually annotated by BRENDA team
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
Int. J. Quantum Chem.
118
e25520
2018
Citrobacter freundii (P45510)
-
Manually annotated by BRENDA team