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
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
BRENDA Link
KEGG Link
MetaCyc Link
pyridoxal 5'-phosphate biosynthesis II
-
-
Vitamin B6 metabolism
-
-
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.
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
btrC2; gene btrC2
UniProt
Manually annotated by BRENDA team
pdxS; gene pdxS
UniProt
Manually annotated by BRENDA team
Bacillus circulans SANK 72073
btrC2; gene btrC2
UniProt
Manually annotated by BRENDA team
Bacillus circulans SANK 72073
pdxS; gene pdxS
UniProt
Manually annotated by BRENDA team
genes pdxS and pdxT
-
-
Manually annotated by BRENDA team
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
gene lmo2101 or pdxS, encoding a subunit of pyridoxal 5'-phosphate synthase
UniProt
Manually annotated by BRENDA team
Pyrococcus horikoshii OT-3
-
SwissProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
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
Q8L1A7, Q8L1A8
a btrC2 disruptant shows deficiency in growth and antibiotic production, and the addition of pyridoxal to the medium restores growth and short-term antibiotics production
malfunction
P9WII9
the disruption of the PdxS gene generates a vitamin B6 auxotrophic Mycobacterium tuberculosis mutant
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
-
malfunction
Bacillus circulans SANK 72073
-
a btrC2 disruptant shows deficiency in growth and antibiotic production, and the addition of pyridoxal to the medium restores growth and short-term antibiotics production
-
malfunction
-
the disruption of the PdxS gene generates a vitamin B6 auxotrophic Mycobacterium tuberculosis mutant
-
metabolism
P9WII9
the organism synthesizes pyridoxal 5'-phosphate via the deoxyxylulose 5-phosphate (DXP)-dependent pathway
physiological function
P9WII9
vitamin B6 biosynthesis is essential for the survival and virulence of Mycobacterium tuberculosis
physiological function
-
vitamin B6 biosynthesis is essential for the survival and virulence of Mycobacterium tuberculosis
-
metabolism
-
the organism synthesizes pyridoxal 5'-phosphate via the deoxyxylulose 5-phosphate (DXP)-dependent pathway
-
additional information
-
proteins PdxS and PdxT interact physically and form the PLP synthase, PdxT is a glutamine amidotransferase subunit that donates an amido group from glutamine to the intermediate of the enzyme reaction
additional information
P9WII9
the overall structure of the protein, composed of a (beta/alpha)8-barrel and two small 310-helices, is quite similar to those of other PdxS proteins. Rv2606c and Rv2604c form a stable complex, suggesting that these proteins might function as pyridoxal biosynthesis lyase and glutamine amidotransferase, respectively
additional information
-
the overall structure of the protein, composed of a (beta/alpha)8-barrel and two small 310-helices, is quite similar to those of other PdxS proteins. Rv2606c and Rv2604c form a stable complex, suggesting that these proteins might function as pyridoxal biosynthesis lyase and glutamine amidotransferase, respectively
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
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
-
-
?
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
-
-
-
?
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
-
-
?
additional information
?
-
Q8L1A7, Q8L1A8
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
-
-
-
additional information
?
-
-
the enzyme catalyzes the conversion of ribose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5'-phosphate
-
-
-
additional information
?
-
Bacillus circulans SANK 72073
Q8L1A7, Q8L1A8
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
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
-
-
?
additional information
?
-
Q8L1A7, Q8L1A8
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
-
-
-
additional information
?
-
-
the enzyme catalyzes the conversion of ribose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5'-phosphate
-
-
-
additional information
?
-
Bacillus circulans SANK 72073
Q8L1A7, Q8L1A8
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
-
-
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
1.0 mM Mn2+, Mg2+, Co2+, Ca2+, Ni2+, Fe3+, Fe2+, Cu3+, Cu2+, or Zn2+ has no effect on activity
additional information
P9WII9
a glycerol molecule is bound at the active site of the enzyme structure through interactions with the conserved residues of Asp29 and Lys86
INHIBITORS
ORGANISM
UNIPROT
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
-
-
D-erythrose 4-phosphate
-
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
PdxR
Q8Y5G2
PdxR is a direct activator of the pdxST operon, has a regulatory function in de novo synthesis of pyridoxal 5'-phosphate, encoded by gene pdxR, PdxR is a member of the MocR/GabR subfamily with an N-terminal putative DNA-binding domain and a C-terminal aminotransferase-like domain. PdxR is also a negative autoregulator, and its ability to repress is increased by pyridoxal 5'-phosphate. PdxR-like proteins, for which PLP plays just a signalling role, form a separate functional group among the MocR/GabRtype proteins. Mutational analysis of the PdxR binding site, overview
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
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]
SUBSTRATE
ORGANISM
UNIPROT
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]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0018
D-ribose 5-phosphate
-
pH 8.0, 37C, mutant enzyme K149R
183
0.0023
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C
183
0.0038
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
183
0.0041
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37C
183
0.0046
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C
183
0.0058
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C
183
0.015
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37C
183
0.0154
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37C
183
0.0172
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37C
183
0.0192
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C
183
0.03
D-ribose 5-phosphate
-
pH 8.0, 37C, wild-type enzyme
183
0.044
D-ribose 5-phosphate
-
pH 8.0, 37C
183
0.00033
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37C
574
0.00058
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
574
0.00077
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37C
574
0.00093
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C
574
0.0019
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C
574
0.0023
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37C
574
0.003
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37C
574
0.0032
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37C
574
0.0039
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37C
574
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
102
0.017
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37C
102
0.018
L-glutamine
-
Pdx2 glutaminase activity, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37C
102
0.021
L-glutamine
-
Pdx2 glutaminase activity, His-tagged wild-type protein, pH 7.5, 37C
102
0.024
L-glutamine
-
Pdx2 glutaminase activity, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37C
102
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
102
0.033
L-glutamine
-
Pdx2 glutaminase activity, R288K mutant Pdx1 protein, pH 7.5, 37C
102
0.128
L-glutamine
-
pH 8.0, 37C
102
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
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]
ORGANISM
UNIPROT
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
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
O31465
assay
37
P37527 and P37528
assay at
PDB
SCOP
CATH
ORGANISM
Plasmodium berghei (strain Anka)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
32830
-
unmodified Pdx1, ESI-MS
726269
200000
-
dynamic light-scattering analysis
721233
363000
C6KT50
analytical ultracentrifugation, 420000 calculated
724999
SUBUNITS
ORGANISM
UNIPROT
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
-
Pdx1, random association pattern of up to 12 Pdx2 subunits to the Pdx1 dodecamer
homododecamer
Q4Z0E8
Pdx1, random association pattern of up to 12 Pdx2 subunits to the Pdx1 dodecamer
homohexamer
-
gel filtration
homohexamer
-
6 * 37014, calculated, dynamic light-scattering analysis
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
additional information
P9WII9
from crystal structure, the asymmetric unit contains 3 Rv2606c molecules, and the dodecameric structure of the protein can be generated by applying crystallographic I222 symmetry, interfaces for the formation of dodecameric structure, overview
additional information
-
from crystal structure, the asymmetric unit contains 3 Rv2606c molecules, and the dodecameric structure of the protein can be generated by applying crystallographic I222 symmetry, interfaces for the formation of dodecameric structure, overview
-
Crystallization/COMMENTARY
ORGANISM
UNIPROT
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
purified recombinant enzyme, hanging drop vapour diffusion method, mixing of 00.0015 ml of 22 mg/ml protein in 20 mM Tris-HCl, pH 8.0, and 5 mM 2-mercaptoethanol, with 0.0015 ml of reservoir solution, containing 8% PEG 8000, 0.1 M 3-[cyclohexylamino]-1-propanesulfonic acid, pH 10.5, and 0.2 M sodium chloride, and equilibration against 0.5 ml of reservoir solution, 20C, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement using the Thermotoga maritima PdxS, PDB code 2ISS
P9WII9
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
LITERATURE
recombinant N-terminally His6-tagged enzyme from Escherichia coli strain B834 by nickel affinity chromatography and cleavage of the tag by TEV protease, followed by anion exchange chromatography and gel filtration to about 95% purity
P9WII9
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
LITERATURE
gene btrC2, DNA and amino acid sequence determination, genetic organization, gene btrC2 is not found in the butirosin-biosynthestic gene cluster, sequence comparison, gene complementation of a btrC2 disruptant by Bacillus subtilis gene pdxT, recombinant expression of untagged BtrC2 in Escherichia coli; gene pdxS, DNA and amino acid sequence determination, genetic organization, recombinant expression of untagged protein encoded by pdxS in Escherichia coli
Q8L1A7, Q8L1A8
expression in Escherichia coli
-
genes pdxS and pdxT, genetic organization, expression of His-tagged PdxT in Escherichia coli
-
Pdx1 and Pdx2 with and without His-tag expressed
-
gene lmo2101 or pdxS, encoding a subunit of pyridoxal 5'-phosphate synthase, quantitative PCR expression analysis, determination of transcription start points of genes pdxS and pdxR, overview
Q8Y5G2
gene Rv2606c, recombinant expression of N-terminally His6-tagged enzyme with a TEV protease cleavage site in Escherichia coli strain B834
P9WII9
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
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
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
H170N
P9WII9
site-directed mutagenesis
H170N
-
site-directed mutagenesis
-
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
additional information
Q8L1A7, Q8L1A8
generation of a gene btrC2 disruptant mutant strain 4-41, which shows deficiency in growth and antibiotic production, and the addition of pyridoxal to the medium restores growth and short-term antibiotics production
additional information
Bacillus circulans SANK 72073
-
generation of a gene btrC2 disruptant mutant strain 4-41, which shows deficiency in growth and antibiotic production, and the addition of pyridoxal to the medium restores growth and short-term antibiotics production
-
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
additional information
Q8Y5G2
construction of a deletion-insertion mutant replacing both the pdxS and pdxT genes with a spectinomycin-resistance cassette, introduction into the chromosome of Listeria monocytogenes strain EGD-e. Cell growth is fully restored by addition of pyridoxal or by complementation of the mutation
H196N
-
Pdx2, catalytically inactive
additional information
-
multiple deletion mutant proteins
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
P9WII9
the enzyme is a target for anti-tuberculosis agents development
drug development
-
the enzyme is a target for anti-tuberculosis agents development
-