4.3.3.6: pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
This is an abbreviated version!
For detailed information about pyridoxal 5'-phosphate synthase (glutamine hydrolysing), go to the full flat file.
Word Map on EC 4.3.3.6
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4.3.3.6
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glutaminase
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ammonia
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amidotransferase
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heteromeric
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deoxyxylulose
-
vitamer
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pentose
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falciparum
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ribulose
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malaria
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eubacteria
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dodecameric
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imine
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oxyanion
-
l-glutamine
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triose
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plasmodial
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hexameric
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drug development
- 4.3.3.6
- glutaminase
- ammonia
-
amidotransferase
-
heteromeric
- deoxyxylulose
-
vitamer
- pentose
- falciparum
- ribulose
- malaria
- eubacteria
-
dodecameric
- imine
-
oxyanion
- l-glutamine
- triose
-
plasmodial
-
hexameric
- drug development
Reaction
Synonyms
Pdx1, PDX2, PdxS, Ph1355, PLP synthase, PLP-synthase complex, PLPS, pyridoxal 5'-phosphate synthase, pyridoxal 5-phosphate synthase, pyridoxal 5-phosphate synthase Snz1, pyridoxal biosynthesis lyase, pyridoxal biosynthesis lyase PdxS, Rv2606c, Snz1
ECTree
4.3.3.6 pyridoxal 5'-phosphate synthase (glutamine hydrolysing)Advanced search results
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results (Substrates Products
Substrates Products on EC 4.3.3.6 - pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
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SUBSTRATE 
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3
pyridoxal 5'-phosphate + 4 H2O + phosphate
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
D-ribulose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
?
-
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
-
-
-
?
ribulose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
-
-
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
-
the enzyme is involved in vitamin B6 biosynthesis
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-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
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
-
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
-
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
-
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
-
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
-
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 + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
-
-
-
?
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
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 + D-glyceraldehyde 3-phosphate + NH3
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
-
in the presence of Pdx1 and Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
-
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
in the presence of Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
in the absence of Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
in the absence of Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
in the absence of Pdx2
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
-
-
-
?
L-glutamine + H2O
L-glutamate + NH3
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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
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-
?
additional information
?
-
-
the enzyme catalyzes the conversion of ribose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5'-phosphate
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-
?
additional information
?
-
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
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-
?
additional information
?
-
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
-
-
?
additional information
?
-
Niallia circulans SANK 72073
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
-
-
?
additional information
?
-
Niallia circulans SANK 72073
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
-
-
?
