Information on EC 4.3.3.6 - pyridoxal 5'-phosphate synthase (glutamine hydrolysing)

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea

EC NUMBER
COMMENTARY
4.3.3.6
-
RECOMMENDED NAME
GeneOntology No.
pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
overall reaction
-
-
-
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
(1b)
-
-
-
L-glutamine + H2O = L-glutamate + NH3
show the reaction diagram
(1a)
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
pyridoxal 5'-phosphate biosynthesis II
-
Vitamin B6 metabolism
-
SYSTEMATIC NAME
IUBMB Comments
D-ribose 5-phosphate,D-glyceraldehyde 3-phosphate pyridoxal 5'-phosphate-lyase
The ammonia is provided by the glutaminase subunit and channeled to the active site of the lyase subunit by a 100 A tunnel. The enzyme can also use ribulose 5-phosphate and dihydroxyacetone phosphate. The enzyme complex is found in aerobic bacteria, archaea, fungi and plants.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Pdx1
-
pyridoxal 5'-phosphate synthase subunit
Pdx1
-
pyridoxal 5'-phosphate synthase complex consits of Pdx1 and Pdx2
PDX2
-
glutaminase subunit
PdxS
O59080
PdxS catalyses the condensation of ribulose 5-phosphate, glyceraldehyde 3-phosphate and ammonia, while glutamine amidotransferase (PdxT) catalyses the production of ammonia from glutamine. PdxS and PdxT form a complex
PdxS
Pyrococcus horikoshii OT-3
O59080
; PdxS catalyses the condensation of ribulose 5-phosphate, glyceraldehyde 3-phosphate and ammonia, while glutamine amidotransferase (PdxT) catalyses the production of ammonia from glutamine. PdxS and PdxT form a complex
-
Ph1355
O59080
gene name
Ph1355
Pyrococcus horikoshii OT-3
O59080
gene name
-
PLP synthase
-
-
PLP synthase
P37527 and P37528
-
PLP-synthase complex
Q4Z0E8
-
PLP-synthase complex
-
-
pyridoxal 5'-phosphate synthase
-
-
pyridoxal 5-phosphate synthase
C6KT50
complex of Pdx1 and Pdx2
pyridoxal 5-phosphate synthase Snz1
Q03148
-
pyridoxal biosynthesis lyase
O59080
-
pyridoxal biosynthesis lyase
Pyrococcus horikoshii OT-3
O59080
-
-
pyridoxal biosynthesis lyase PdxS
O59080
-
pyridoxal biosynthesis lyase PdxS
Pyrococcus horikoshii OT-3
O59080
-
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
P37527: pyridoxal 5'-phosphate synthase subunit Pdx1 (pdxS), and P37528: glutaminase subunit Pdx2 (PdxT)
P37527 and P37528
SwissProt
Manually annotated by BRENDA team
Pdx2, glutaminase subunit
SwissProt
Manually annotated by BRENDA team
Corynebacterium glutamicum NJ0898
-
-
-
Manually annotated by BRENDA team
Pyrococcus horikoshii OT-3
-
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
malfunction
-
deletion of the pdxST genes in Corynebacterium glutamicum NJ0898 results in vitamin B6 auxotrophy, which is restored by external pyridoxal, pyridoxal 5'-phosphate or pyridoxamine
malfunction
Corynebacterium glutamicum NJ0898
-
deletion of the pdxST genes in Corynebacterium glutamicum NJ0898 results in vitamin B6 auxotrophy, which is restored by external pyridoxal, pyridoxal 5'-phosphate or pyridoxamine
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
-
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
the enzyme is involved in vitamin B6 biosynthesis
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
O31465
L-glutamine binding triggers a cascade of conformational changes of Pdx2 (glutaminase subunit) that leads to a structure favorable for Pdx1 (pyridoxal 5'-phosphate synthase subunit) binding
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
mechanistic studies. Pdx2 has glutaminase activity and channels ammonia to the active site of the PLP synthase subunit, Pdx1, where ribose-5-phosphate, glyceraldehyde-3-phosphate, and ammonia are condensed in a complex series of reactions. Under pre-steady-state conditions, a chromophoric intermediate is observed that accumulates upon addition of only two of the substrates, D-ribose 5-phosphate and glutamine. The intermediate is covalently bound to the protein. The phosphate unit of R5P is eliminated rather than hydrolyzed in route to intermediate formation
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
preference of D-ribose 5-phosphate compared to D-ribulose 5-phosphate. Characterization of a novel chromophoric reaction intermediate. The chromophoric group of this intermediate is appended to the epsilon-amino group of Lys81 and that the new residue has the composition C5H6O2, corresponding to the elimination of one equivalent of inorganic phosphate, one molecule of water one additional proton from the original protonated imine adduct
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
the ammonia generated at the YaaE active site is channelled to the active site of YaaD where pyridoxal 5'-phosphate formation occurs
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
the synthase subunit of this enzyme, Pdx1, operates in concert with the glutaminase subunit, Pdx2, to catalyze the complex condensation of ribose 5-phosphate, glutamine and glyceraldehyde 3-phosphate to form pyridoxal 5'-phosphate. Many if not all of the reaction intermediates are covalently bound to the synthase subunit, thus making them difficult to isolate and characterize. By denaturing the enzyme at points along the reaction coordinate, the structures of three covalently bound intermediates are solved. Thes analysis reveals a 1,5 migration of the lysine amine linking the intermediate to the enzyme during the conversion of ribose 5-phosphate to pyridoxal 5'-phosphate
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
two proteins form a complex that functions as a glutamine amidotransferase, with YaaE as the glutaminase domain and YaaD as the acceptor and pyridoxal 5'-phosphate synthesis domain. The synthase reaction can also utilize an external ammonium source but, in contrast to other glutamine amidotransferases, is dependent on YaaE under certain conditions
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
-
two proteins form a complex that functions as a glutamine amidotransferase, with YaaE as the glutaminase domain and YaaD as the acceptor and pyridoxal 5'-phosphate synthesis domain. Both the glutaminase and synthase reactions are dependent on the respective protein partner. The synthase reaction can also utilize an external ammonium source but, in contrast to other glutamine amidotransferases, is dependent on YaaE under certain conditions
-
-
?
D-ribose 5-phosphate + glyceraldehyd 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
-
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
Q4Z0E8
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
in the presence of Pdx1 and Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
C6KT50
in the presence of Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
-
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
-
in the absence of Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
C6KT50
in the absence of Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
Q4Z0E8
in the absence of Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
Pyrococcus horikoshii OT-3
-
-
-
-
?
D-ribulose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
?
show the reaction diagram
-
preference of D-ribose 5-phosphate compared to D-ribulose 5-phosphate
-
-
?
L-glutamine + H2O
L-glutamate + NH3
show the reaction diagram
-
two proteins form a complex that functions as a glutamine amidotransferase, with YaaE as the glutaminase domain and YaaD as the acceptor and pyridoxal 5'-phosphate synthesis domain. Glutaminase activity of YaaE is only detected in the presence of its partner protein YaaD. A 1:1 stoichiometry of both proteins appears to be optimal for activity
-
-
?
ribulose 5-phosphate + glyceraldehyde 3-phosphate + NH3
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
O59080, -
-
-
-
?
ribulose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
Q03148, -
-
-
-
?
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
the enzyme is involved in vitamin B6 biosynthesis
-
-
?
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
1.0 mM Mn2+, Mg2+, Co2+, Ca2+, Ni2+, Fe3+, Fe2+, Cu3+, Cu2+, or Zn2+ has no effect on activity
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
2-deoxy-D-ribose 5-phosphate
-
at 12 mM 56% residual activity
4-phospho-D-erythronhydrazide
-
-
acivicin
-
inhibition of the glutaminase domain YuaaD, and thus pyridoxal 5'-phosphate synthesis
D-erythronhydrazide
-
-
-
D-erythrose 4-phosphate
-
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.077
-
D-glyceraldehyde 3-phosphate
-
pH 8.0, 37C
0.026
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C
0.032
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37C
0.035
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
0.04
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C; pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37C
0.043
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C; pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37C
0.044
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C
0.068
-
D-ribose 5-phosphate
-
pH 8.0, 37C
0.122
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37C
0.126
-
D-ribose 5-phosphate
-
pH 8.0, 37C, wild-type enzyme
0.185
-
D-ribose 5-phosphate
-
pH 8.0, 37C, mutant enzyme K149R
0.155
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37C
0.186
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37C
0.195
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37C
0.22
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37C
0.229
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
0.249
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C
0.262
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C
0.267
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C
0.307
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C
0.93
-
L-glutamine
-
Pdx2 glutaminase activity, R288K mutant Pdx1 protein, pH 7.5, 37C
0.99
-
L-glutamine
-
pH 8.0, 37C
1.12
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C
1.16
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged wild-type protein, pH 7.5, 37C; Pdx2 glutaminase activity, wild-type protein, pH 7.5, 37C
1.2
-
L-glutamine
-
Pdx2 glutaminase activity, R288A mutant Pdx1 protein, pH 7.5, 37C
1.31
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C
1.33
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
1.44
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C
1.54
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0001
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C
0.00013
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
0.0002
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C; pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C
0.00033
-
D-ribose 5-phosphate
-
pH 8.0, 37C
0.00033
-
D-ribose 5-phosphate
-
pH 8.0, 37C, mutant enzyme K149R
0.0005
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C; pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37C
0.00055
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37C
0.0006
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37C
0.00062
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37C
0.00067
-
D-ribose 5-phosphate
-
pH 8.0, 37C, free pyridoxal 5'-phosphate synthase subunit (Pdx1)
0.004
-
D-ribose 5-phosphate
-
pH 8.0, 37C, wild-type enzyme
0.0007
-
D-ribulose 5-phosphate
-
pH 8.0, 37C, free pyridoxal 5'-phosphate synthase subunit (Pdx1)
0.022
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
0.024
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C; Pdx2 glutaminase activity, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C; Pdx2 glutaminase activity, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C; Pdx2 glutaminase activity, His-tagged wild-type protein, pH 7.5, 37C
0.026
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C
0.0295
-
L-glutamine
-
Pdx2 glutaminase activity, wild-type protein, pH 7.5, 37C
0.0305
-
L-glutamine
-
Pdx2 glutaminase activity, R288A mutant Pdx1 protein, pH 7.5, 37C
0.0307
-
L-glutamine
-
Pdx2 glutaminase activity, R288K mutant Pdx1 protein, pH 7.5, 37C
0.127
-
L-glutamine
-
pH 8.0, 37C
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0018
-
D-ribose 5-phosphate
-
pH 8.0, 37C, mutant enzyme K149R
9351
0.0023
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C
9351
0.0038
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
9351
0.0041
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37C
9351
0.0046
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C
9351
0.0058
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C
9351
0.015
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37C
9351
0.0154
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37C
9351
0.0172
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37C
9351
0.0192
-
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C
9351
0.03
-
D-ribose 5-phosphate
-
pH 8.0, 37C, wild-type enzyme
9351
0.044
-
D-ribose 5-phosphate
-
pH 8.0, 37C
9351
0.00033
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C
11067
0.00058
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
11067
0.00077
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C
11067
0.00093
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C
11067
0.0019
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C
11067
0.0023
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37C
11067
0.003
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37C
11067
0.0032
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37C
11067
0.0039
-
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37C
11067
0.016
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C; Pdx2 glutaminase activity, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C
12226
0.017
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
12226
0.018
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C
12226
0.021
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged wild-type protein, pH 7.5, 37C
12226
0.024
-
L-glutamine
-
Pdx2 glutaminase activity, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C
12226
0.026
-
L-glutamine
-
Pdx2 glutaminase activity, R288A mutant Pdx1 protein, pH 7.5, 37C; Pdx2 glutaminase activity, wild-type protein, pH 7.5, 37C
12226
0.033
-
L-glutamine
-
Pdx2 glutaminase activity, R288K mutant Pdx1 protein, pH 7.5, 37C
12226
0.128
-
L-glutamine
-
pH 8.0, 37C
12226
IC50 VALUE [mM]
IC50 VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.016
-
4-phospho-D-erythronhydrazide
-
Pdx1 in the heteromeric pyridoxal 5'-phosphate synthase complex, pH 8.0, 37C
0.043
-
4-phospho-D-erythronhydrazide
-
Pdx1, pH 8.0, 37C
0.902
-
D-erythronhydrazide
-
Pdx1, pH 8.0, 37C
-
160
-
D-Erythrose
-
Pdx1, pH 8.0, 37C
3.7
-
D-erythrose 4-phosphate
-
Pdx1, pH 8.0, 37C
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.00025
-
C6KT50
DELTA 279-301 protein, in the presence of Pdx2, pH 8.0, 37C
0.00025
-
Q4Z0E8
L82A mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.00031
-
Q4Z0E8
M103A mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.00042
-
Q4Z0E8
M103A mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0007
-
-
Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.000779
-
C6KT50
wild-type protein, in the presence of Pdx2, pH 8.0, 37C
0.0008
-
Q4Z0E8
M148L mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0009
-
Q4Z0E8
Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37C; Plasmodium falciparum Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0009
-
-
Pdx1/Plasmodium berghei Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0011
-
Q4Z0E8
Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0012
-
Q4Z0E8
L82A mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0013
-
Q4Z0E8
Pdx1/Plasmodium falciparum Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0013
-
-
Plasmodium berghei Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0015
-
Q4Z0E8
M46I mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0018
-
Q4Z0E8
M19V mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.002
-
Q4Z0E8
M19V mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0028
-
Q4Z0E8
M46I mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.0037
-
Q4Z0E8
M148L mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37C
0.087
-
Q4Z0E8
M19V mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
0.115
-
Q4Z0E8
L82A mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
0.126
-
Q4Z0E8
M103F mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
0.15
-
Q4Z0E8
Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
0.175
-
Q4Z0E8
Plasmodium falciparum Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
0.175
-
-
Pdx1/Plasmodium berghei Pdx2 complex, glutaminase activity, pH 8, 30C
0.178
-
Q4Z0E8
M103A mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
0.229
-
Q4Z0E8
M148L mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
0.233
-
Q4Z0E8
Pdx1/Plasmodium falciparum Pdx2 complex, glutaminase activity, pH 8, 30C
0.233
-
-
Plasmodium berghei Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
0.26
-
-
Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
0.284
-
Q4Z0E8
M46I mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30C
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
37
-
O31465
assay
37
-
-
assay at
37
-
P37527 and P37528
assay at
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
32830
-
-
unmodified Pdx1, ESI-MS
200000
-
-
dynamic light-scattering analysis
363000
-
C6KT50
analytical ultracentrifugation, 420000 calculated
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dodecamer
C6KT50
12 * 29000, two interacting hexamers, analytical ultracentrifugation, 35320.7 Da determined by ESI-MS
hexamer
-
PdxS exists as a hexamer or dodecamer depending on species and makes a 1:1 complex with PdxT. Pyrococcus horikoshii PdxS forms hexamer in solution. It has a 37 amino acids insertion region, which is found in some archaeal PdxS proteins. This additional insertion perturbs dodecamer formation of Pyrococcus horikoshii PdxS
hexamer
Pyrococcus horikoshii OT-3
-
PdxS exists as a hexamer or dodecamer depending on species and makes a 1:1 complex with PdxT. Pyrococcus horikoshii PdxS forms hexamer in solution. It has a 37 amino acids insertion region, which is found in some archaeal PdxS proteins. This additional insertion perturbs dodecamer formation of Pyrococcus horikoshii PdxS
-
homododecamer
Q4Z0E8
Pdx1, random association pattern of up to 12 Pdx2 subunits to the Pdx1 dodecamer
homododecamer
-
Pdx1, random association pattern of up to 12 Pdx2 subunits to the Pdx1 dodecamer
homohexamer
-
6 * 37014, calculated, dynamic light-scattering analysis
homohexamer
-
gel filtration
homohexamer
Pyrococcus horikoshii OT-3
-
gel filtration
-
additional information
P37527 and P37528
the pyridoxal 5'-phosphate synthase complex is made up of 24 protein units assembled like a cogwheel, a dodecameric Pdx1 to which 12 Pdx2 subunits attach. Macromolecular assembly is directed by an N-terminalalpha-helix on the synthase. Interaction with the synthase subunit leads to glutaminase activation, resulting in formation of an oxyanion hole, a prerequisite for catalysis
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
hanging-drop vapor diffusion, 3D structure of the pyridoxal 5'-phosphate synthase complex with substrate glutamine bound as well as those of the individual synthase and glutaminase subunits Pdx1 and Pdx2, respectively. The complex is made up of 24 protein units assembled like a cogwheel, a dodecameric Pdx1 to which 12 Pdx2 subunits attach. Macromolecular assembly is directed by an N-terminalalpha-helix on the synthase. Interaction with the synthase subunit leads to glutaminase activation, resulting in formation of an oxyanion hole, a prerequisite for catalysis
P37527 and P37528
Pdx1, chimeric complex of Pdx1 and Pdx2 from Plasmodium falciparum
Q4Z0E8
chimeric complex of Pdx2 and Pdx1 from Plasmodium berghei
-
2-methyl-2,4-pentanediol; crystallized at 23C using 2-methyl-2,4-pentanediol as a precipitant. Crystals of apo and ribose 5'-phosphate complex forms of PdxS diffract to 2.7 A and 3.1 A resolution, respectively, and belong to the monoclinic space group P2(1)
-
crystallization at 22C using 2-methyl-2,4-pentanediol as a precipitant. Crystals of PdxS diffract to 2.61 A resolution and belong to the monoclinic space group P2(1), with unit-cell parameters a = 59.30, b = 178.56, c = 109.23 A, beta = 102.97. The asymmetric unit contained six monomers; hanging-drop vapour-diffusion method, 296 K, 2-methyl-2,4-pentanediol
-
hanging-drop vapour diffusion method, 16C
Q03148, -
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
immobilized metal ion affinity chromatography (Ni2+), gel filtration
Q4Z0E8
affinity chromatography using the Strep-Tag
-
immobilized metal ion affinity chromatography (Ni2+), gel filtration
-
ion exchange chromatography (Q Sepharose), gel filtration
-
immobilized metal ion affinity chromatography (Ni2+), gel filtration
Q03148, -
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression in Escherichia coli
-
Pdx1 and Pdx2 with and without His-tag expressed
-
His-tagged subunits Pdx1 and Pdx2 expressed in Escherichia coli BL21-CodonPlus (DE3)-RIL
Q4Z0E8
His-tagged protein expressed in Escherichia coli BL21-CodonPlus(DE3)-RIL
C6KT50
His-tagged subunits Pdx1 and Pdx2 expressed in Escherichia coli BL21-CodonPlus (DE3)-RIL
-
Strep-Tag-fusion proteins expressed in Escherichia coli BLR (DE3)
-
expressed in Escherichia coli Rosetta2 (DE3) pLysS; overexpressed in Escherichia coli strain Rosetta2 (DE3)
-
expressed in Escherichia coli Rosetta2 (DE3) pLysS; overexpression in Escherichia coli
-
His-tagged protein expressed in Escherichia coli BL21 (DE3)
Q03148, -
EXPRESSION
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression of pdxS and pdxT is significantly reduced in the presence of pyridoxal or pyridoxal 5'-phosphate, whereas supplementing with pyridoxamine or pyridoxine shows no effect on pdxST expression
-
the transcription regulator PdxR controls the biosynthesis of pyridoxal or pyridoxal 5'-phosphate in Corynebacterium glutamicum by activating the expression of the pyridoxal or pyridoxal 5'-phosphate synthase genes pdxST
-
expression of pdxS and pdxT is significantly reduced in the presence of pyridoxal or pyridoxal 5'-phosphate, whereas supplementing with pyridoxamine or pyridoxine shows no effect on pdxST expression
Corynebacterium glutamicum NJ0898
-
-
the transcription regulator PdxR controls the biosynthesis of pyridoxal or pyridoxal 5'-phosphate in Corynebacterium glutamicum by activating the expression of the pyridoxal or pyridoxal 5'-phosphate synthase genes pdxST
Corynebacterium glutamicum NJ0898
-
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
D99A
O31465
mutant of Pdx1 (pyridoxal 5'-phosphate synthase subunit), 5% of the pyridoxal 5'-phosphate synthase activity compared to wild-type enzyme with L-glutamine as N-donor, 17.2% of the glutaminase activity compared to wild-type enzyme
E105D
-
Pdx1
E15A
O31465
mutant of Pdx2 (glutaminase subunit), 280% of the glutaminase activity compared to wild-type activity, Pdx2 (glutaminase subunit) complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
E48A
O31465
mutant of Pdx2 (glutaminase subunit), no glutaminase activity in complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
H115A
-
Pdx1
H115A/R138A
-
Pdx1
H170N
-
catalytically incompetent mutant of glutaminase subunit Pdx2
H170N
-
Pdx2, catalytically inert
K149A
-
mutant enzyme does not form an adduct with ribulose-5-phosphate
K149A
-
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
K149R
-
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) retains the ability to form the imine adduct
K187A
-
Pdx1, 84% of wild-type activity
K18A
O31465
mutant of Pdx1 (pyridoxal 5'-phosphate synthase subunit), 40.5% of the pyridoxal 5'-phosphate synthase activity compared to wild-type enzyme with L-glutamine as N-donor, 64.5% of the glutaminase activity compared to wild-type enzyme
K81A
-
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
K81R
-
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
Q10A
O31465
mutant of Pdx2 (glutaminase subunit), 94% of the glutaminase activity compared to wild-type activity, Pdx2 (glutaminase subunit) complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
Q10E
O31465
mutant of Pdx2 (glutaminase subunit), 2% of the glutaminase activity compared to wild-type activity, Pdx2 (glutaminase subunit) complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
Q10N
O31465
mutant of Pdx2 (glutaminase subunit), 34% of the glutaminase activity compared to wild-type activity, Pdx2 (glutaminase subunit) complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
R106A
O31465
mutant of Pdx2 (glutaminase subunit), no glutaminase activity in complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
R135A
O31465
mutant of Pdx2 (glutaminase subunit), no glutaminase activity in complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
R138A
-
Pdx1
R288A
-
Pdx1, able to activate Pdx2
R288K
-
Pdx1, able to activate Pdx2
S75A
O31465
mutant of Pdx1 (pyridoxal 5'-phosphate synthase subunit), 51% of the pyridoxal 5'-phosphate synthase activity compared to wild-type enzyme with L-glutamine as N-donor, 84% of the glutaminase activity compared to wild-type enzyme
H199N
Q4Z0E8
Pdx2
L82A
Q4Z0E8
Pdx1
M103A
Q4Z0E8
Pdx1
M103F
Q4Z0E8
Pdx1
M148L
Q4Z0E8
Pdx1
M19V
Q4Z0E8
Pdx1
M46I
Q4Z0E8
Pdx1
D26A/K83A/K151A
-
no formation of an internal chromophore with characteristic absorbance at 320 nm during reaction (observed with wild type protein)
DELTA 270-301
C6KT50
mainly monomer, Pdx2 activation, no pyridoxal 5'-phosphate synthesis
DELTA 273-301
C6KT50
dodecamer, Pdx2 activation, no pyridoxal 5'-phosphate synthesis
DELTA 279-301
C6KT50
dodecamer, Pdx2 activation, reduced pyridoxal 5'-phosphate synthesis
DELTA 287-301
C6KT50
dodecamer, Pdx2 activation, precipitates upon addition of glyceraldehyd 3-phosphate
DELTA 293-301
C6KT50
behaviour like DELTA 287-301
DELTA 295-301
C6KT50
behaviour like DELTA 287-301
E136A/R139A/R140A
-
formation of an internal chromophore with characteristic absorbance at 320 nm during reaction (also observed with wild type protein)
R167A
-
reduced formation of an internal chromophore with characteristic absorbance at 320 nm during reaction (observed with wild type protein), 50% wild type activity
R85A/H88A/E91A
-
no formation of an internal chromophore with characteristic absorbance at 320 nm during reaction (observed with wild type protein), dodecameric assembly prevented
S270A/DELTA 273-301
C6KT50
dodecamer
E116A
Q03148, -
activity as the wild-type protein
K117A
Q03148, -
no synthesis of pyridoxal 5'-phosphate, capacity to catalyse dihydroxyacetone phosphate isomerization
K148A
Q03148, -
no synthesis of pyridoxal 5'-phosphate, capacity to catalyse dihydroxyacetone phosphate isomerization
K240A
Q03148, -
activity as the wild-type protein
R136A/R137A
Q03148, -
no synthesis of pyridoxal 5'-phosphate, dihydroxyacetone phosphate isomerization activity as the wild-type protein
R164A
Q03148, -
completely inactive, dihydroxyacetone phosphate isomerization activity as the wild-type protein
H196N
-
Pdx2, catalytically inactive
additional information
-
multiple deletion mutant proteins