View source for Pyridoxine 5'-phosphate synthase

{{Short description|Class of enzymes}}
{{enzyme
| Name = Pyridoxine 5'-phosphate synthase
| EC_number = 2.6.99.2
| CAS_number = 
| GO_code = 
| image =Pyridoxine 5'-phosphate synthase (1M5W).png 
| caption =''Escherichia coli'' pyridoxine 5'-phosphate synthase {{PDB|1M5W}} 
|name=Pyridoxine 5'-phosphate synthase|image_size=240}}
In [[enzymology]], a '''pyridoxine 5'-phosphate synthase''' ({{EC number|2.6.99.2}}) is an [[enzyme]] that [[catalysis|catalyzes]] the [[chemical reaction]]

:1-deoxy-D-xylulose 5-phosphate + 3-hydroxy-1-aminoacetone phosphate <math>\rightleftharpoons</math> pyridoxine-5'-phosphate + phosphate + 2 H<sub>2</sub>O

The two [[substrate (biochemistry)|substrates]] of this enzyme are [[1-deoxy-D-xylulose 5-phosphate]] (DXP) and [[3-hydroxy-1-aminoacetone phosphate]] (HAP), whereas its 3 [[product (chemistry)|products]] are [[water|H<sub>2</sub>O]], [[phosphate]], and pyridoxine-5'-phosphate (a vitamer of [[pyridoxal phosphate]]).

== Mechanism ==

[[File:PdxJ mechanism.png|thumb|Arrow-pushing mechanism of the reaction catalyzed by pdxJ.<ref name = Garrido-Franco2002>{{cite journal | vauthors = Garrido-Franco M, Laber B, Huber R, Clausen T | title = Enzyme-ligand complexes of pyridoxine 5'-phosphate synthase: implications for substrate binding and catalysis | journal = Journal of Molecular Biology | volume = 321 | issue = 4 | pages = 601–12 | date = August 2002 | pmid = 12206776 | doi = 10.1016/S0022-2836(02)00695-2 }}</ref> Other mechanisms have been proposed<ref>{{cite journal | vauthors = Mukherjee T, Hanes J, Tews I, Ealick SE, Begley TP | title = Pyridoxal phosphate: biosynthesis and catabolism | journal = Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics | volume = 1814 | issue = 11 | pages = 1585–96 | date = November 2011 | pmid = 21767669 | doi = 10.1016/j.bbapap.2011.06.018 }}</ref> but differ only in the timing of [[phosphate]] removal.]]

In the first step of this [[condensation reaction]], the [[amine]] group of HAP forms a [[Schiff base]] with the [[ketone group]] of DXP. The [[hydroxy group|hydroxyl group]] on C4 of DXP is eliminated, forming an [[enol]]. The enol eliminates the phosphate derived from DXP, and water is added to the resulting double bond to reform the [[enol]]. This enol then attacks the HAP [[ketone group]] to close the ring and the resulting [[hydroxy group|hydroxyl group]] is eliminated to form a [[double bond]]. A deprotonation causes the ring to [[aromatic ring|aromatize]], completing the synthesis of pyridoxine-5'-phosphate.

3-hydroxy-1-aminoacetone phosphate is unstable, so the [[reaction mechanism]] cannot be confirmed directly. Nonetheless, <sup>14</sup>C and <sup>18</sup>O [[isotopic labeling]] experiments,<ref name = Cane1999>{{cite journal | vauthors = Cane DE, Du S, Robinson J | date = 1999 | title = Biosynthesis of vitamin B6: Enzymatic conversion of 1-deoxy-D-xylulose-5-phosphate to pyridoxol phosphate | journal = J. Am. Chem. Soc. | volume = 121 | pages = 7722&ndash;23 | doi = 10.1021/ja9914947 | issue = 33 }}</ref><ref>{{cite journal | vauthors = Cane DE, Du S, Spenser ID | date = 2000 | title = Biosynthesis of vitamin B6: Origin of the oxygen atoms of pyridoxol phosphate | journal = J. Am. Chem. Soc. | volume = 122 | pages = 4213&ndash;14 | doi = 10.1021/ja000224h | issue = 17 }}</ref> as well as [[protein structure|structural]] studies,<ref name = Garrido-Franco2002/><ref name = Garrido-Franco2001>{{cite journal | vauthors = Franco MG, Laber B, Huber R, Clausen T | title = Structural basis for the function of pyridoxine 5'-phosphate synthase | journal = Structure | volume = 9 | issue = 3 | pages = 245–53 | date = March 2001 | pmid = 11286891 | doi = 10.1016/S0969-2126(01)00584-6 | doi-access = free }}</ref> support the mechanism shown here. A [[glutamate]] residue, Glu72, is positioned ideally to perform most of the [[acid-base catalysis]] required in this mechanism, with [[histidine]] residues His45 and His193 appearing to play roles as well.

== Structure ==
Pyridoxine-5'-phosphate synthase, or pdxJ, is a [[TIM barrel]] protein, although it exhibits some departures from this motif. Most significantly, the central tunnel of pdxJ is [[hydrophilic]] in contrast to the [[hydrophobic]] central tunnel observed in most TIM barrel proteins, and pdxJ has three extra [[alpha helix|alpha helices]] compared to the classical TIM fold.<ref name = Garrido-Franco2003>{{cite journal | vauthors = Garrido-Franco M | title = Pyridoxine 5'-phosphate synthase: de novo synthesis of vitamin B6 and beyond | journal = Biochimica et Biophysica Acta | volume = 1647 | issue = 1–2 | pages = 92–7 | date = April 2003 | pmid = 12686115 | doi = 10.1016/s1570-9639(03)00065-7 }}</ref> These three extra helices are important for mediating inter-subunit contacts in the assembled [[octamer]].<ref>{{cite journal | vauthors = Fitzpatrick TB, Amrhein N, Kappes B, Macheroux P, Tews I, Raschle T | title = Two independent routes of de novo vitamin B6 biosynthesis: not that different after all | journal = The Biochemical Journal | volume = 407 | issue = 1 | pages = 1–13 | date = October 2007 | pmid = 17822383 | doi = 10.1042/bj20070765 | pmc = 2267407 }}</ref> However, there are also important similarities in function: like many [[TIM barrel]] proteins, pdxJ binds its substrates primarily by their [[phosphate]] moieties,<ref name = Garrido-Franco2002/><ref name = Garrido-Franco2001/> and the phosphate-binding site responsible for binding to HAP and pyridoxine 5'-phosphate is a conserved motif found in many [[TIM barrel]] proteins.<ref>{{cite journal | vauthors = Nagano N, Orengo CA, Thornton JM | title = One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions | journal = Journal of Molecular Biology | volume = 321 | issue = 5 | pages = 741–65 | date = August 2002 | pmid = 12206759 | doi = 10.1016/S0022-2836(02)00649-6 }}</ref> The fact that pdxJ binds [[substrate (chemistry)|substrates]] through their phosphate groups explains a previously discovered specificity for the substrates over their respective non-phosphorylated alcohols.<ref name = Cane1999/><ref>{{cite journal | vauthors = Laber B, Maurer W, Scharf S, Stepusin K, Schmidt FS | title = Vitamin B6 biosynthesis: formation of pyridoxine 5'-phosphate from 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose-5-phosphate by PdxA and PdxJ protein | journal = FEBS Letters | volume = 449 | issue = 1 | pages = 45–8 | date = April 1999 | pmid = 10225425 | doi = 10.1016/S0014-5793(99)00393-2 | s2cid = 33542088 | doi-access = free }}</ref>

pdxJ exhibits several different [[protein structure|conformations]], 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 HAP [[structural analog|analog]] are bound, loop 4 of the protein folds over the active site, preventing the escape of [[reaction intermediates]] or undesirable side reactions.<ref name = Garrido-Franco2002/><ref name = Garrido-Franco2001/> Binding of phosphate alone is not capable of causing a transition between the open and closed states.<ref name = Garrido-Franco2003/> A third, "partially open" intermediate has also been reported upon binding of DXP alone.<ref>{{cite journal |vauthors=Yeh JI, Du S, Pohl E, Cane DE | date = 2002 | title = Multistate binding in pyridoxine 5′-phosphate synthase: 1.96 Å crystal structure in complex with 1-deoxy-D-xylulose phosphate | journal = Biochemistry  | volume = 41 | pages = 11649&ndash;57  | issue = 39| doi=10.1021/bi026292t| pmid = 12269807 }}</ref>

pdxJ assembles as an [[oligomer|octamer]] under biological conditions.<ref name = Garrido-Franco2003/><ref>{{cite journal |vauthors=Garrido-Franco M, Huber R, Schmidt FS, et al | date = 2000 | title = Crystallization and preliminary X-ray crystallographic analysis of PdxJ, the pyridoxine 50-phosphate synthesizing enzyme | journal = Acta Crystallographica  | volume = 56 | issue = 8 | pages = 1045&ndash;48  | doi=10.1107/S0907444900007368| pmid = 10944349 | doi-access =  }}</ref> 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, an [[arginine]] residue Arg20 forms part of the [[active site]] in the other monomer, where it helps bind both [[phosphate]] groups.<ref name = Garrido-Franco2001/>

== Classification ==

This enzyme belongs to the family of [[transferase]]s, specifically those transferring nitrogenous groups transferring other nitrogenous groups.

== Nomenclature ==

The [[List of enzymes|systematic name]] of this enzyme class is '''1-deoxy-D-xylulose-5-phosphate:3-amino-2-oxopropyl phosphate 3-amino-2-oxopropyltransferase (phosphate-hydrolysing; cyclizing)'''. Other names in common use include '''pyridoxine 5-phosphate phospho lyase''', '''PNP synthase''', and '''PdxJ'''.

== Biological role ==

This enzyme participates in [[vitamin B6|vitamin B<sub>6</sub> metabolism]]. pdxJ plays a role in the [[vitamin B6|DXP-dependent pathway]] of pyridoxal phosphate. The DXP-dependent pathway is found predominantly in [[Gammaproteobacteria]] and some [[Alphaproteobacteria]].<ref name = Mittenhuber2001>{{cite journal | vauthors = Mittenhuber G | title = Phylogenetic analyses and comparative genomics of vitamin B6 (pyridoxine) and pyridoxal phosphate biosynthesis pathways | journal = Journal of Molecular Microbiology and Biotechnology | volume = 3 | issue = 1 | pages = 1–20 | date = January 2001 | pmid = 11200221 }}</ref> Because of this distribution, pdxJ has been identified as a potential [[biological target|drug target]] for [[antibiotics]].<ref name=Mittenhuber2001/> This identification seems to have validity, as other approaches have also identified pdxJ as a good target for [[drug]] development.<ref>{{cite journal | vauthors = Ahmad S, Raza S, et al | date = 2018 | title = From phylogeny to protein dynamics: A computational hierarchical quest for potent drug identification against an emerging enteropathogen "Yersinia enterocolitica". | journal = Journal of Molecular Liquids | volume = 265 | pages = 372&ndash;89  | doi = 10.1016/j.molliq.2018.06.013 | s2cid = 90481778 }}</ref> However, there may be limits to this approach as pdxJ is not found in obligate parasites.<ref name = Mittenhuber2001/> pdxJ and more generally vitamin B<sub>6</sub> metabolism in the [[microbiome]] have also been shown to alter the effects of certain compounds on [[animal]] hosts.<ref>{{cite journal | vauthors = Scott TA, Quintaneiro LM, Norvaisas P, Lui PP, Wilson MP, Leung KY, Herrera-Dominguez L, Sudiwala S, Pessia A, Clayton PT, Bryson K, Velagapudi V, Mills PB, Typas A, Greene ND, Cabreiro F | display-authors = 6 | title = Host-Microbe Co-metabolism Dictates Cancer Drug Efficacy in C. elegans | journal = Cell | volume = 169 | issue = 3 | pages = 442–456.e18 | date = April 2017 | pmid = 28431245 | pmc = 5406385 | doi = 10.1016/j.cell.2017.03.040}}</ref>

== References ==
{{reflist|30em}}

{{Nitrogenous transferases}}
{{Enzymes}}
{{Portal bar|Biology|border=no}}

[[Category:EC 2.6.99]]
[[Category:Enzymes of unknown structure]]