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Information on EC 4.3.3.6 - pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
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4.3.3.6 pyridoxal 5'-phosphate synthase (glutamine hydrolysing)IUBMB Comments
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.
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Word Map
- 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
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Reaction Schemes
Synonyms
plp synthase, rv2606c, pyridoxal biosynthesis lyase, ph1355, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Pdx1
PdxS
Ph1355
PLP synthase
PLP-synthase complex
pyridoxal 5'-phosphate synthase
pyridoxal biosynthesis lyase
pyridoxal biosynthesis lyase PdxS
Rv2606c
Pdx1
-
pyridoxal 5'-phosphate synthase complex consits of Pdx1 and Pdx2
PdxS
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
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
-
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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
overall reaction
-
-
-
D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5'-phosphate + 4 H2O + phosphate
(1b)
-
-
-
L-glutamine + H2O = L-glutamate + NH3
(1a)
-
-
-
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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.
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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
-
-
?
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
-
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
?
-
-
the enzyme catalyzes the conversion of ribose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5'-phosphate
-
-
?
additional information
?
-
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
-
-
?
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
-
-
?
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NATURAL SUBSTRATE
NATURAL 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 + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
-
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
-
-
-
?
additional information
?
-
-
the enzyme catalyzes the conversion of ribose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5'-phosphate
-
-
?
additional information
?
-
BtrC2 shows no catalytic activity as 2-deoxy-scyllo-inosose (DOI) synthase
-
-
?
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
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
-
1.0 mM Mn2+, Mg2+, Co2+, Ca2+, Ni2+, Fe3+, Fe2+, Cu3+, Cu2+, or Zn2+ has no effect on activity
additional information
a glycerol molecule is bound at the active site of the enzyme structure through interactions with the conserved residues of Asp29 and Lys86
additional information
-
a glycerol molecule is bound at the active site of the enzyme structure through interactions with the conserved residues of Asp29 and Lys86
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INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
acivicin
-
inhibition of the glutaminase domain YuaaD, and thus pyridoxal 5'-phosphate synthesis
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
PdxR
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
-
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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Malaria
Exploring inhibition of Pdx1, a component of the PLP synthase complex of the human malaria parasite Plasmodium falciparum.
Tuberculosis
Cloning, expression, purification, crystallization and X-ray crystallographic analysis of Rv2606c from Mycobacterium tuberculosis H37Rv.
Tuberculosis
Crystal structure of Mycobacterium tuberculosis Rv2606c: a pyridoxal biosynthesis lyase.
Tuberculosis
Transposon mutagenesis of Mycobacterium marinum identifies a locus linking pigmentation and intracellular survival.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.026
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37°C
0.032
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37°C
0.035
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37°C
0.04
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37°C
0.04
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37°C
0.043
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37°C
0.043
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37°C
0.044
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37°C
0.122
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37°C
0.155
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37°C
0.186
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37°C
0.195
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37°C
0.22
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37°C
0.229
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37°C
0.249
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37°C
0.262
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37°C
0.267
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37°C
0.307
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37°C
0.93
L-glutamine
-
Pdx2 glutaminase activity, R288K mutant Pdx1 protein, pH 7.5, 37°C
1.12
L-glutamine
-
Pdx2 glutaminase activity, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37°C
1.16
L-glutamine
-
Pdx2 glutaminase activity, His-tagged wild-type protein, pH 7.5, 37°C
1.16
L-glutamine
-
Pdx2 glutaminase activity, wild-type protein, pH 7.5, 37°C
1.2
L-glutamine
-
Pdx2 glutaminase activity, R288A mutant Pdx1 protein, pH 7.5, 37°C
1.31
L-glutamine
-
Pdx2 glutaminase activity, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37°C
1.33
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37°C
1.44
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37°C
1.54
L-glutamine
-
Pdx2 glutaminase activity, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37°C
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0007
D-ribulose 5-phosphate
-
pH 8.0, 37°C, free pyridoxal 5'-phosphate synthase subunit (Pdx1)
0.0001
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37°C
0.00013
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37°C
0.0002
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37°C
0.0002
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37°C
0.0005
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37°C
0.0005
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37°C
0.00055
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37°C
0.0006
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37°C
0.00062
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37°C
0.00067
D-ribose 5-phosphate
-
pH 8.0, 37°C, free pyridoxal 5'-phosphate synthase subunit (Pdx1)
0.022
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37°C
0.024
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37°C
0.024
L-glutamine
-
Pdx2 glutaminase activity, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37°C
0.024
L-glutamine
-
Pdx2 glutaminase activity, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37°C
0.024
L-glutamine
-
Pdx2 glutaminase activity, His-tagged wild-type protein, pH 7.5, 37°C
0.026
L-glutamine
-
Pdx2 glutaminase activity, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37°C
0.0295
L-glutamine
-
Pdx2 glutaminase activity, wild-type protein, pH 7.5, 37°C
0.0305
L-glutamine
-
Pdx2 glutaminase activity, R288A mutant Pdx1 protein, pH 7.5, 37°C
0.0307
L-glutamine
-
Pdx2 glutaminase activity, R288K mutant Pdx1 protein, pH 7.5, 37°C
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0023
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37°C
0.0038
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37°C
0.0041
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37°C
0.0046
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37°C
0.0058
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37°C
0.015
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37°C
0.0154
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37°C
0.0172
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37°C
0.0192
D-ribose 5-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37°C
0.00033
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37°C
0.00058
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37°C
0.00077
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37°C
0.00093
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37°C
0.0019
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37°C
0.0023
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288A mutant Pdx1 protein, pH 7.5, 37°C
0.003
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, wild-type protein, pH 7.5, 37°C
0.0032
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, R288K mutant Pdx1 protein, pH 7.5, 37°C
0.0039
glyceraldehyde 3-phosphate
-
pyridoxal 5'-phosphate formation, His-tagged wild-type protein, pH 7.5, 37°C
0.016
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A/R138A mutant Pdx1 protein, pH 7.5, 37°C
0.016
L-glutamine
-
Pdx2 glutaminase activity, His-tagged R138A mutant Pdx1 protein, pH 7.5, 37°C
0.017
L-glutamine
-
Pdx2 glutaminase activity, His-tagged H115A mutant Pdx1 protein, pH 7.5, 37°C
0.018
L-glutamine
-
Pdx2 glutaminase activity, His-tagged K187A mutant Pdx1 protein, pH 7.5, 37°C
0.021
L-glutamine
-
Pdx2 glutaminase activity, His-tagged wild-type protein, pH 7.5, 37°C
0.024
L-glutamine
-
Pdx2 glutaminase activity, His-tagged E105D mutant Pdx1 protein, pH 7.5, 37°C
0.026
L-glutamine
-
Pdx2 glutaminase activity, R288A mutant Pdx1 protein, pH 7.5, 37°C
0.026
L-glutamine
-
Pdx2 glutaminase activity, wild-type protein, pH 7.5, 37°C
0.033
L-glutamine
-
Pdx2 glutaminase activity, R288K mutant Pdx1 protein, pH 7.5, 37°C
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.016
4-phospho-D-erythronhydrazide
Plasmodium falciparum
-
Pdx1 in the heteromeric pyridoxal 5'-phosphate synthase complex, pH 8.0, 37°C
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.00025
0.00031
M103A mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.00042
M103A mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0007
-
Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.000779
wild-type protein, in the presence of Pdx2, pH 8.0, 37°C
0.0008
M148L mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0009
0.0011
Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0012
L82A mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0013
0.0015
M46I mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0018
M19V mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.002
M19V mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0028
M46I mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0037
M148L mutant Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.087
M19V mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
0.115
L82A mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
0.126
M103F mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
0.175
0.178
M103A mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
0.229
M148L mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
0.233
0.284
M46I mutant Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
0.00025
L82A mutant Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.00025
DELTA 279-301 protein, in the presence of Pdx2, pH 8.0, 37°C
0.0009
Pdx1, NH4Cl as NH3+ donor, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0009
Plasmodium falciparum Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0009
-
Pdx1/Plasmodium berghei Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0013
Pdx1/Plasmodium falciparum Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.0013
-
Plasmodium berghei Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.175
Plasmodium falciparum Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
0.175
-
Pdx1/Plasmodium berghei Pdx2 complex, glutaminase activity, pH 8, 30°C
0.233
Pdx1/Plasmodium falciparum Pdx2 complex, glutaminase activity, pH 8, 30°C
0.233
-
Plasmodium berghei Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
37
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Q5L3Y2: subunit PdxS, Q5L3Y1: subunit PdxT
SwissProt
brenda
gene lmo2101 or pdxS, encoding a subunit of pyridoxal 5'-phosphate synthase
UniProt
brenda
Niallia circulans SANK 72073
P37527: pyridoxal 5'-phosphate synthase subunit Pdx1 (pdxS), and P37528: glutaminase subunit Pdx2 (PdxT)
SwissProt
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
metabolism
physiological function
additional information
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
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
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
Niallia 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
the organism synthesizes pyridoxal 5'-phosphate via the deoxyxylulose 5-phosphate (DXP)-dependent pathway
metabolism
-
the organism synthesizes pyridoxal 5'-phosphate via the deoxyxylulose 5-phosphate (DXP)-dependent pathway
-
physiological function
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
-
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
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
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
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
29000
12 * 29000, two interacting hexamers, analytical ultracentrifugation, 35320.7 Da determined by ESI-MS
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SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dodecamer
12 * 29000, two interacting hexamers, analytical ultracentrifugation, 35320.7 Da determined by ESI-MS
hexamer
homododecamer
homohexamer
oligomer
the intact enzyme includes 12 synthase and 12 glutaminase subunits
additional information
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
-
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
-
Pdx1, random association pattern of up to 12 Pdx2 subunits to the Pdx1 dodecamer
homohexamer
6 * 37014, calculated, dynamic light-scattering analysis
additional information
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
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
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
-
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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
sitting drop vapor diffusion, to investigate the mechanism of the synthase subunit, crystal structures are obtained for three intermediate states of the Geobacillus stearothermophilus intact PLPS or its synthase subunit. The structures capture the synthase active site at three distinct steps in its complicated catalytic cycle, provide insights into the elusive mechanism, and illustrate the coordinated motions within the synthase subunit that separate the catalytic states
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, 20°C, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement using the Thermotoga maritima PdxS, PDB code 2ISS
Pdx1, chimeric complex of Pdx1 and Pdx2 from Plasmodium falciparum
crystallization at 22°C 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
crystallized at 23°C 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)
hanging-drop vapour-diffusion method, 296 K, 2-methyl-2,4-pentanediol
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D99A
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
E15A
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
mutant of Pdx2 (glutaminase subunit), no glutaminase activity in complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
H170N
K149A
K149R
-
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) retains the ability to form the imine adduct
K18A
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
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
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
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
mutant of Pdx2 (glutaminase subunit), no glutaminase activity in complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
R135A
mutant of Pdx2 (glutaminase subunit), no glutaminase activity in complex with Pdx1 (pyridoxal 5'-phosphate synthase subunit)
S75A
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
H170N
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
mainly monomer, Pdx2 activation, no pyridoxal 5'-phosphate synthesis
DELTA 273-301
dodecamer, Pdx2 activation, no pyridoxal 5'-phosphate synthesis
DELTA 279-301
dodecamer, Pdx2 activation, reduced pyridoxal 5'-phosphate synthesis
DELTA 287-301
dodecamer, Pdx2 activation, precipitates upon addition of glyceraldehyd 3-phosphate
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
K117A
no synthesis of pyridoxal 5'-phosphate, capacity to catalyse dihydroxyacetone phosphate isomerization
K148A
no synthesis of pyridoxal 5'-phosphate, capacity to catalyse dihydroxyacetone phosphate isomerization
R136A/R137A
no synthesis of pyridoxal 5'-phosphate, dihydroxyacetone phosphate isomerization activity as the wild-type protein
R164A
completely inactive, dihydroxyacetone phosphate isomerization activity as the wild-type protein
additional information
K149A
-
mutant of pyridoxal 5'-phosphate synthase subunit (Pdx1) does not form the imine adduct
additional information
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
additional information
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
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
Niallia 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
-
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PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
immobilized metal ion affinity chromatography (Ni2+), gel filtration
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
immobilized metal ion affinity chromatography (Ni2+), gel filtration
immobilized metal ion affinity chromatography (Ni2+), gel filtration
immobilized metal ion affinity chromatography (Ni2+), gel filtration
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli Rosetta2 (DE3) pLysS
expression in Escherichia coli
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 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
gene pdxS, DNA and amino acid sequence determination, genetic organization, recombinant expression of untagged protein encoded by pdxS in Escherichia coli
gene Rv2606c, recombinant expression of N-terminally His6-tagged enzyme with a TEV protease cleavage site in Escherichia coli strain B834
genes pdxS and pdxT, genetic organization, expression of His-tagged PdxT in Escherichia coli
-
His-tagged protein expressed in Escherichia coli BL21-CodonPlus(DE3)-RIL
His-tagged subunits Pdx1 and Pdx2 expressed in Escherichia coli BL21-CodonPlus (DE3)-RIL
His-tagged subunits Pdx1 and Pdx2 expressed in Escherichia coli BL21-CodonPlus (DE3)-RIL
-
His-tagged subunits Pdx1 and Pdx2 expressed in Escherichia coli BL21-CodonPlus (DE3)-RIL
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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
-
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
-
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
-
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
drug development
drug development
the enzyme is a target for anti-tuberculosis agents development
drug development
-
the enzyme is a target for anti-tuberculosis agents development
-
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Hanes, J.W.; Keresztes, I.; Begley, T.P.
Trapping of a chromophoric intermediate in the Pdx1-catalyzed biosynthesis of pyridoxal 5'-phosphate
Angew. Chem. Int. Ed. Engl.
47
2102-2105
2008
Bacillus subtilis
brenda
Wallner, S.; Neuwirth, M.; Flicker, K.; Tews, I.; Macheroux, P.
Dissection of contributions from invariant amino acids to complex formation and catalysis in the heteromeric pyridoxal 5-phosphate synthase complex from Bacillus subtilis
Biochemistry
48
1928-1935
2009
Bacillus subtilis (O31465), Bacillus subtilis
brenda
Burns, K.E.; Xiang, Y.; Kinsland, C.L.; McLafferty, F.W.; Begley, T.P.
Reconstitution and biochemical characterization of a new pyridoxal-5'-phosphate biosynthetic pathway
J. Am. Chem. Soc.
127
3682-3683
2005
Bacillus subtilis
brenda
Raschle, T.; Amrhein, N.; Fitzpatrick, T.B.
On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis
J. Biol. Chem.
280
32291-32300
2005
Bacillus subtilis
brenda
Raschle, T.; Arigoni, D.; Brunisholz, R.; Rechsteiner, H.; Amrhein, N.; Fitzpatrick, T.B.
Reaction mechanism of pyridoxal 5'-phosphate synthase. Detection of an enzyme-bound chromophoric intermediate
J. Biol. Chem.
282
6098-6105
2007
Bacillus subtilis
brenda
Jochmann, N.; Gtker, S.; Tauch, A.
Positive transcriptional control of the pyridoxal phosphate biosynthesis genes pdxST by the MocR-type regulator PdxR of Corynebacterium glutamicum ATCC 13032
Microbiology
157
77-88
2011
Corynebacterium glutamicum, Corynebacterium glutamicum NJ0898
brenda
Hanes, J.W.; Keresztes, I.; Begley, T.P.
13C NMR snapshots of the complex reaction coordinate of pyridoxal phosphate synthase
Nat. Chem. Biol.
4
425-430
2008
Bacillus subtilis
brenda
Strohmeier, M.; Raschle, T.; Mazurkiewicz, J.; Rippe, K.; Sinning, I.; Fitzpatrick, T.B.; Tews, I.
Structure of a bacterial pyridoxal 5'-phosphate synthase complex
Proc. Natl. Acad. Sci. USA
103
19284-19289
2006
Bacillus subtilis (P37527 and P37528)
brenda
Yoon, J.Y.; Park, C.R.; Lee, H.H.; Suh, S.W.
Overexpression, crystallization and preliminary X-ray crystallographic analysis of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii
Acta Crystallogr. Sect. F
68
440-442
2012
Pyrococcus horikoshii, Pyrococcus horikoshii (O59080), Pyrococcus horikoshii OT-3 (O59080)
brenda
Matsuura, A.; Yoon, J.Y.; Yoon, H.J.; Lee, H.H.; Suh, S.W.
Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii
Mol. Cells
34
407-412
2012
Pyrococcus horikoshii (O59080), Pyrococcus horikoshii, Pyrococcus horikoshii OT-3 (O59080)
brenda
Zhang, X.; Teng, Y.; Liu, J.; He, Y.; Zhou, K.; Chen, Y.; Zhou, C.
Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1
Biochem. J.
432
445-450
2010
Saccharomyces cerevisiae (Q03148), Saccharomyces cerevisiae
brenda
Reeksting, S.; Mller, I.; Burger, P.; Burgos, E.; Salmon, L.; Louw, A.; Birkholtz, L.; Wrenger, C.
Exploring inhibition of Pdx1, a component of the PLP synthase complex of the human malaria parasite Plasmodium falciparum
Biochem. J.
449
175-187
2013
Plasmodium falciparum
brenda
Derrer, B.; Windeisen, V.; Guedez Rodriguez, G.; Seidler, J.; Gengenbacher, M.; Lehmann, W.; Rippe, K.; Sinning, I.; Tews, I.; Kappes, B.
Defining the structural requirements for ribose 5-phosphate-binding and intersubunit cross-talk of the malarial pyridoxal 5-phosphate synthase
FEBS Lett.
584
4169-4174
2010
Plasmodium falciparum (C6KT50)
brenda
Moccand, C.; Kaufmann, M.; Fitzpatrick, T.
It takes two to Tango: Defining an essential second active site in pyridoxal 5'-phosphate synthase
PLoS ONE
6
e16042
2011
Bacillus subtilis
brenda
Guedez, G.; Hipp, K.; Windeisen, V.; Derrer, B.; Gengenbacher, M.; Bttcher, B.; Sinning, I.; Kappes, B.; Tews, I.
Assembly of the eukaryotic PLP-synthase complex from Plasmodium and activation of the Pdx1 enzyme
Structure
20
172-184
2012
Plasmodium falciparum, Plasmodium berghei (A0A509AM71)
brenda
Kim, S.; Kim, K.J.
Crystal structure of Mycobacterium tuberculosis Rv2606c: a pyridoxal biosynthesis lyase
Biochem. Biophys. Res. Commun.
435
255-259
2013
Mycobacterium tuberculosis (P9WII9), Mycobacterium tuberculosis, Mycobacterium tuberculosis H37Rv (P9WII9)
brenda
Itagaki, S.; Haga, M.; Oikawa, Y.; Sakoda, A.; Ohke, Y.; Sawada, H.; Eguchi, T.; Tamegai, H.
Differences in the roles of a glutamine amidotransferase subunit of pyridoxal 5'-phosphate synthase between Bacillus circulans and Bacillus subtilis
Biosci. Biotechnol. Biochem.
77
1481-1485
2013
Bacillus subtilis, Niallia circulans (Q8L1A7), Niallia circulans (Q8L1A8), Niallia circulans SANK 72073 (Q8L1A7), Niallia circulans SANK 72073 (Q8L1A8)
brenda
Belitsky, B.R.
Role of PdxR in the activation of vitamin B6 biosynthesis in Listeria monocytogenes
Mol. Microbiol.
92
1113-1128
2014
Listeria monocytogenes (Q8Y5G2)
brenda
Smith, A.M.; Brown, W.C.; Harms, E.; Smith, J.L.
Crystal structures capture three states in the catalytic cycle of a pyridoxal phosphate (PLP) synthase
J. Biol. Chem.
290
5226-5239
2015
Geobacillus kaustophilus (Q5L3Y2 AND Q5L3Y1)
brenda
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Release 2023.1 (January 2023)
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