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Information on EC 4.3.3.6 - pyridoxal 5'-phosphate synthase (glutamine hydrolysing) and Organism(s) Plasmodium falciparum and UniProt Accession C6KT50

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EC Tree
     4 Lyases
         4.3 Carbon-nitrogen lyases
             4.3.3 Amine-lyases
                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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This record set is specific for:
Plasmodium falciparum
UNIPROT: C6KT50
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The taxonomic range for the selected organisms is: Plasmodium falciparum
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Synonyms
plp synthase, rv2606c, pyridoxal biosynthesis lyase, ph1355, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pyridoxal 5-phosphate synthase
complex of Pdx1 and Pdx2
Pdx1
-
pyridoxal 5'-phosphate synthase complex consits of Pdx1 and Pdx2
PLP-synthase complex
-
-
PATHWAY SOURCE
PATHWAYS
-
-
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.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
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 Pdx2
-
-
?
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 + L-glutamine
pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate
show the reaction diagram
-
-
-
-
?
D-ribose 5-phosphate + glyceraldehyde 3-phosphate + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-deoxy-D-ribose 5-phosphate
-
at 12 mM 56% residual activity
4-phospho-D-erythronhydrazide
-
-
D-erythronhydrazide
-
-
D-erythrose
-
-
D-erythrose 4-phosphate
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.016 - 0.043
4-phospho-D-erythronhydrazide
0.902
D-erythronhydrazide
Plasmodium falciparum
-
Pdx1, pH 8.0, 37°C
160
D-erythrose
Plasmodium falciparum
-
Pdx1, pH 8.0, 37°C
3.7
D-erythrose 4-phosphate
Plasmodium falciparum
-
Pdx1, pH 8.0, 37°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.00025
DELTA 279-301 protein, in the presence of Pdx2, pH 8.0, 37°C
0.000779
wild-type protein, in the presence of Pdx2, pH 8.0, 37°C
0.0007
-
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
-
Plasmodium berghei Pdx1/Pdx2 complex, pyridoxal 5'-phosphate synthesis, pH 8, 37°C
0.175
-
Pdx1/Plasmodium berghei Pdx2 complex, glutaminase activity, pH 8, 30°C
0.233
-
Plasmodium berghei Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
0.26
-
Pdx1/Pdx2 complex, glutaminase activity, pH 8, 30°C
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
29000
12 * 29000, two interacting hexamers, analytical ultracentrifugation, 35320.7 Da determined by ESI-MS
363000
analytical ultracentrifugation, 420000 calculated
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dodecamer
12 * 29000, two interacting hexamers, analytical ultracentrifugation, 35320.7 Da determined by ESI-MS
homododecamer
-
Pdx1, random association pattern of up to 12 Pdx2 subunits to the Pdx1 dodecamer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
chimeric complex of Pdx2 and Pdx1 from Plasmodium berghei
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
DELTA 293-301
behaviour like DELTA 287-301
DELTA 295-301
behaviour like DELTA 287-301
S270A/DELTA 273-301
dodecamer
D26A/K83A/K151A
-
no formation of an internal chromophore with characteristic absorbance at 320 nm during reaction (observed with wild type protein)
E136A/R139A/R140A
-
formation of an internal chromophore with characteristic absorbance at 320 nm during reaction (also observed with wild type protein)
H196N
-
Pdx2, catalytically inactive
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
additional information
-
multiple deletion mutant proteins
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
immobilized metal ion affinity chromatography (Ni2+), gel filtration
affinity chromatography using the Strep-Tag
-
immobilized metal ion affinity chromatography (Ni2+), gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
-
Strep-Tag-fusion proteins expressed in Escherichia coli BLR (DE3)
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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 berghei (A0A509AM71), Plasmodium falciparum
Manually annotated by BRENDA team