_EC 2.6.99.2 Pyridoxine 5'-phosphate synthase. 11 PDB entries  
EC 2.-.-.- Transferases. [17,943 PDB entries]
EC 2.6.-.- Transferring nitrogenous groups. [555 PDB entries]
EC 2.6.99.- Transferring other nitrogenous groups. [22 PDB entries]
EC 2.6.99.2 Pyridoxine 5'-phosphate synthase. [11 PDB entries]    
1ho1

Reaction: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = pyridoxine 5'-phosphate + phosphate + 2 H(2)O.
 


1-deoxy-D-xylulose 5-phosphate
+
3-amino-2-oxopropyl phosphate
=
pyridoxine 5'-phosphate
+
phosphate
+ 2 × H(2)O
Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Other name(s): Pnp synthase. Pyridoxine 5-phosphate phospho lyase.
Comments: In Escherichia coli, the coenzyme pyridoxal 5'-phosphate is synthesized de novo by a pathway that involves Ec 1.2.1.72, Ec 1.1.1.290, Ec 2.6.1.52, Ec 1.1.1.262, Ec 2.6.99.2 and Ec 1.4.3.5. 1-deoxy-D-xylulose cannot replace 1-deoxy-D-xylulose 5-phosphate as a substrate.
Links:   [IntEnz]   [ExPASy]   [KEGG]  

There are 11 PDB entries in enzyme class E.C.2.6.99.2

  PDB code Protein
1ho1
Crystal structure of pyridoxine 5'-phosphate synthase
Source: Escherichia coli. Organism_taxid: 562. Gene: pdxj. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (235 residues) CATH domain: 3.20.20.70
1ho4
Crystal structure of pyridoxine 5'-phosphate synthase in com pyridoxine 5'-phosphate and inorganic phosphate
Source: Escherichia coli. Organism_taxid: 562. Gene: pdxj. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (242 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group PXP corresponds to enzyme product Pyridoxine
  Het Group PO4 corresponds to enzyme product phosphate
1ixn
Enzyme-substrate complex of pyridoxine 5'-phosphate synthase
Source: Escherichia coli. Organism_taxid: 562. Gene: pdxj. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (242 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group DXP corresponds to enzyme reactant 1-deoxy-D-xylulose
  Het Group G3P is 50.00% similar to enzyme product phosphate
1ixo
Enzyme-analogue substrate complex of pyridoxine 5'-phosphate
Source: Escherichia coli. Organism_taxid: 562. Gene: pdxj. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (235 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group G3P is 81.82% similar to enzyme reactant 3-amino-2-oxopropyl
1ixp
Enzyme-phosphate complex of pyridoxine 5'-phosphate synthase
Source: Escherichia coli. Organism_taxid: 562. Gene: pdxj. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (242 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group PO4 corresponds to enzyme product phosphate
1ixq
Enzyme-phosphate2 complex of pyridoxine 5'-phosphate synthas
Source: Escherichia coli. Organism_taxid: 562. Gene: pdxj. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (235 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group PO4 corresponds to enzyme product phosphate
1m5w
1.96 a crystal structure of pyridoxine 5'-phosphate synthase complex with 1-deoxy-d-xylulose phosphate
Source: Escherichia coli. Organism_taxid: 562. Gene: pdxj. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Chains: A, B, C, D, E, F, G, H (242 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group DXP corresponds to enzyme reactant 1-deoxy-D-xylulose
  Het Group PO4 corresponds to enzyme product phosphate
3f4n
Crystal structure of pyridoxal phosphate biosynthetic protei from yersinia pestis
Source: Yersinia pestis. Organism_taxid: 632. Strain: co92. Gene: pdxj, y1300, ypo2930, yp_2525. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: n-terminal his-tag with tev protease cut-sit
Chains: A, B, C, D, E, F, G, H (242 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group PXP corresponds to enzyme product Pyridoxine
3gk0
Crystal structure of pyridoxal phosphate biosynthetic protei burkholderia pseudomallei
Source: Burkholderia pseudomallei. Organism_taxid: 320372. Strain: 1710b. Gene: pdxj. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D, E, F, G, H (252 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group DXP corresponds to enzyme reactant 1-deoxy-D-xylulose
  Het Group PO4 corresponds to enzyme product phosphate
3o6c
Pyridoxal phosphate biosynthetic protein pdxj from campyloba jejuni
Source: Campylobacter jejuni subsp. Jejuni. Organism_taxid: 192222. Strain: nctc 11168. Gene: cj1238, pdxj. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Chain: A (259 residues) CATH domain: 3.20.20.70
Bound ligand:   Het Group PO4 corresponds to enzyme product phosphate
3o6d
Pyridoxal phosphate biosynthetic protein pdxj from campyloba jejuni in complex with pyridoxine-5'-phosphate
Source: Campylobacter jejuni subsp. Jejuni. Organism_taxid: 192222. Strain: nctc 11168. Gene: cj1238, pdxj. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Chain: A (259 residues) CATH domain: 3.20.20.70
Bound ligands:   Het Group PXP corresponds to enzyme product Pyridoxine 5'-phosphate
  Het Group PO4 corresponds to enzyme product phosphate