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Information on EC 4.3.3.6 - pyridoxal 5'-phosphate synthase (glutamine hydrolysing) and Organism(s) Bacillus subtilis and UniProt Accession P37527

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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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Bacillus subtilis
UNIPROT: P37527 not found.
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Word Map
The taxonomic range for the selected organisms is: Bacillus subtilis
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
Pdx1
-
pyridoxal 5'-phosphate synthase subunit
PDX2
-
glutaminase subunit
PLP synthase
pyridoxal 5'-phosphate synthase
-
-
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 + 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 + 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 + 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-ribulose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine
?
show the reaction diagram
-
preference of D-ribose 5-phosphate compared to D-ribulose 5-phosphate
-
-
?
L-glutamine + H2O
L-glutamate + NH3
show the reaction diagram
-
two proteins form a complex that functions as a glutamine amidotransferase, with YaaE as the glutaminase domain and YaaD as the acceptor and pyridoxal 5'-phosphate synthesis domain. Glutaminase activity of YaaE is only detected in the presence of its partner protein YaaD. A 1:1 stoichiometry of both proteins appears to be optimal for activity
-
-
?
additional information
?
-
-
the enzyme catalyzes the conversion of ribose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5'-phosphate
-
-
?
NATURAL SUBSTRATE
NATURAL 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 + 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
?
-
-
the enzyme catalyzes the conversion of ribose 5-phosphate and glyceraldehyde 3-phosphate to pyridoxal 5'-phosphate
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
1.0 mM Mn2+, Mg2+, Co2+, Ca2+, Ni2+, Fe3+, Fe2+, Cu3+, Cu2+, or Zn2+ has no effect on activity
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
acivicin
-
inhibition of the glutaminase domain YuaaD, and thus pyridoxal 5'-phosphate synthesis
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.077
D-glyceraldehyde 3-phosphate
-
pH 8.0, 37°C
0.026 - 0.185
D-ribose 5-phosphate
0.155 - 0.307
glyceraldehyde 3-phosphate
0.93 - 1.54
L-glutamine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0001 - 0.004
D-ribose 5-phosphate
0.0007
D-ribulose 5-phosphate
-
pH 8.0, 37°C, free pyridoxal 5'-phosphate synthase subunit (Pdx1)
0.022 - 0.127
L-glutamine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0018 - 0.044
D-ribose 5-phosphate
0.00033 - 0.0039
glyceraldehyde 3-phosphate
0.016 - 0.128
L-glutamine
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
A0A3A5HYD7_BACIU
196
0
21513
TrEMBL
-
A0A4R6HC64_BACIU
196
0
21504
TrEMBL
-
Q2Y2R1_BACIU
294
0
31612
TrEMBL
-
A0A3A5HYA6_BACIU
294
0
31597
TrEMBL
-
A0A7U5ATD2_BACIU
196
0
21516
TrEMBL
-
A0A6A8FM32_BACIU
196
0
21375
TrEMBL
-
A0A8B5NHZ5_BACIU
196
0
21490
TrEMBL
-
A0A063XB46_BACIU
196
0
21447
TrEMBL
-
A0A8I1WKE6_BACIU
294
0
31640
TrEMBL
-
A0A0M0KST8_BACIU
196
0
21503
TrEMBL
-
A0A0D5D179_BACIU
294
0
31628
TrEMBL
-
A0A7U5ATD4_BACIU
294
0
31612
TrEMBL
-
A0A5D4MZB4_BACIU
294
0
31627
TrEMBL
-
A0A5D4N020_BACIU
196
0
21482
TrEMBL
-
A0A5F2KF99_BACIU
196
0
21516
TrEMBL
-
A0A4R6HCL5_BACIU
294
0
31628
TrEMBL
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32830
-
unmodified Pdx1, ESI-MS
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
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
E105D
-
Pdx1
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)
H115A
-
Pdx1
H115A/R138A
-
Pdx1
H170N
K149A
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
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)
R138A
-
Pdx1
R288A
-
Pdx1, able to activate Pdx2
R288K
-
Pdx1, able to activate Pdx2
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
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
-
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team
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
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team