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Information on EC 4.3.3.6 - pyridoxal 5'-phosphate synthase (glutamine hydrolysing) and Organism(s) Pyrococcus horikoshii and UniProt Accession O59080

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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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Pyrococcus horikoshii
UNIPROT: O59080
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Word Map
The taxonomic range for the selected organisms is: Pyrococcus horikoshii
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 biosynthesis lyase
-
pyridoxal biosynthesis lyase PdxS
-
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 + NH4+
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
-
-
-
?
ribulose 5-phosphate + glyceraldehyde 3-phosphate + NH3
pyridoxal 5'-phosphate + 4 H2O + phosphate
show the reaction diagram
-
-
-
?
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
200000
dynamic light-scattering analysis
37014
6 * 37014, calculated, dynamic light-scattering analysis
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
homohexamer
gel filtration
homohexamer
6 * 37014, calculated, dynamic light-scattering analysis
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
2-methyl-2,4-pentanediol
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
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
ion exchange chromatography (Q Sepharose), gel filtration
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli Rosetta2 (DE3) pLysS
overexpressed in Escherichia coli strain Rosetta2 (DE3)
overexpression in Escherichia coli
expressed in Escherichia coli Rosetta2 (DE3) pLysS
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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)
Manually annotated by BRENDA team
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)
Manually annotated by BRENDA team