| Pyridoxine 5'-phosphate synthase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
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| Identifiers | |||||||||
| EC no. | 2.6.99.2 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDBPDBePDBsum | ||||||||
| |||||||||
Inenzymology, apyridoxine 5'-phosphate synthase (EC2.6.99.2) is anenzyme thatcatalyzes thechemical reaction
The twosubstrates of this enzyme are1-deoxy-D-xylulose 5-phosphate (DXP) and3-hydroxy-1-aminoacetone phosphate (HAP), whereas its 3products areH2O,phosphate, and pyridoxine-5'-phosphate (a vitamer ofpyridoxal phosphate).
In the first step of thiscondensation reaction, theamine group of HAP forms aSchiff base with theketone group of DXP. Thehydroxyl group on C4 of DXP is eliminated, forming anenol. The enol eliminates the phosphate derived from DXP, and water is added to the resulting double bond to reform theenol. This enol then attacks the HAPketone group to close the ring and the resultinghydroxyl group is eliminated to form adouble bond. A deprotonation causes the ring toaromatize, completing the synthesis of pyridoxine-5'-phosphate.
3-hydroxy-1-aminoacetone phosphate is unstable, so thereaction mechanism cannot be confirmed directly. Nonetheless,14C and18Oisotopic labeling experiments,[3][4] as well asstructural studies,[1][5] support the mechanism shown here. Aglutamate residue, Glu72, is positioned ideally to perform most of theacid-base catalysis required in this mechanism, withhistidine residues His45 and His193 appearing to play roles as well.
Pyridoxine-5'-phosphate synthase, or pdxJ, is aTIM barrel protein, although it exhibits some departures from this motif. Most significantly, the central tunnel of pdxJ ishydrophilic in contrast to thehydrophobic central tunnel observed in most TIM barrel proteins, and pdxJ has three extraalpha helices compared to the classical TIM fold.[6] These three extra helices are important for mediating inter-subunit contacts in the assembledoctamer.[7] However, there are also important similarities in function: like manyTIM barrel proteins, pdxJ binds its substrates primarily by theirphosphate moieties,[1][5] and the phosphate-binding site responsible for binding to HAP and pyridoxine 5'-phosphate is a conserved motif found in manyTIM barrel proteins.[8] The fact that pdxJ bindssubstrates through their phosphate groups explains a previously discovered specificity for the substrates over their respective non-phosphorylated alcohols.[3][9]
pdxJ exhibits several differentconformations, depending on the substrates or substrate analogs bound. The first state, exhibited when pdxJ has either pyridoxine-5'-phosphate or no substrates bound, is classified as the "open" conformation. This conformation is characterized by an active site freely accessible by solvent. In contrast, when DXP and an HAPanalog are bound, loop 4 of the protein folds over the active site, preventing the escape ofreaction intermediates or undesirable side reactions.[1][5] Binding of phosphate alone is not capable of causing a transition between the open and closed states.[6] A third, "partially open" intermediate has also been reported upon binding of DXP alone.[10]
pdxJ assembles as anoctamer under biological conditions.[6][11] This octamer can be thought of as a tetramer of dimers, and it is likely that the dimer is the active unit of the protein. In each dimer, anarginine residue Arg20 forms part of theactive site in the other monomer, where it helps bind bothphosphate groups.[5]
This enzyme belongs to the family oftransferases, specifically those transferring nitrogenous groups transferring other nitrogenous groups.
Thesystematic name of this enzyme class is1-deoxy-D-xylulose-5-phosphate:3-amino-2-oxopropyl phosphate 3-amino-2-oxopropyltransferase (phosphate-hydrolysing; cyclizing). Other names in common use includepyridoxine 5-phosphate phospho lyase,PNP synthase, andPdxJ.
This enzyme participates invitamin B6 metabolism. pdxJ plays a role in theDXP-dependent pathway of pyridoxal phosphate. The DXP-dependent pathway is found predominantly inGammaproteobacteria and someAlphaproteobacteria.[12] Because of this distribution, pdxJ has been identified as a potentialdrug target forantibiotics.[12] This identification seems to have validity, as other approaches have also identified pdxJ as a good target fordrug development.[13] However, there may be limits to this approach as pdxJ is not found in obligate parasites.[12] pdxJ and more generally vitamin B6 metabolism in themicrobiome have also been shown to alter the effects of certain compounds onanimal hosts.[14]
