View source for Phosphopentose epimerase

{{short description|Class of enzymes}}
{{infobox enzyme
| Name       = ribulose-phosphate 3-epimerase
| EC_number  = 5.1.3.1
| CAS_number = 9024-20-8
| GO_code    = 0004750
| image      = 3inp.jpg
| width      = 270
| caption    = D-ribulose-5-phosphate 3-epimerase dodekamer, ''Francisella tularensis''
}}
{{Pfam_box 
| Symbol = Ribul_P_3_epim 
| Name = Ribulose-phosphate 3 epimerase family 
| image = 
| width = 
| caption = 
| Pfam= PF00834
| InterPro= IPR000056
| SMART= 
| Prosite = PDOC00833
| SCOP = 1rpx
| TCDB = 
| OPM family= 
| OPM protein= 
| PDB= 
{{PDB3|1tqj}}B:6-208     {{PDB3|1rpx}}A:58-260    {{PDB3|1h1z}}A:8-208
{{PDB3|1h1y}}B:8-208     {{PDB3|1tqx}}A:7-208
}}

'''Phosphopentose epimerase''' (also known as '''ribulose-phosphate 3-epimerase''' and '''ribulose 5-phosphate 3-epimerase''', {{EnzExplorer|5.1.3.1}}) encoded in humans by the ''RPE'' gene<ref>{{cite web|url=https://www.genecards.org/cgi-bin/carddisp.pl?gene=RPE|title=''RPE'' Gene - Ribulose-5-Phosphate-3-Epimerase|website=GeneCards|date=3 April 2024|access-date=11 May 2024}}</ref> is a [[metalloprotein]] that catalyzes the interconversion between D-ribulose 5-phosphate and D-xylulose 5-phosphate.<ref name=Akana /> 
:D-ribulose 5-phosphate <math>\rightleftharpoons</math> D-xylulose 5-phosphate

This reversible conversion is required for [[carbon fixation]] in plants – through the [[Calvin cycle]] – and for the nonoxidative phase of the [[pentose phosphate pathway]].<ref name=Liang>{{cite journal | vauthors = Liang W, Ouyang S, Shaw N, Joachimiak A, Zhang R, Liu ZJ | title = Conversion of D-ribulose 5-phosphate to D-xylulose 5-phosphate: new insights from structural and biochemical studies on human RPE | journal = FASEB Journal | volume = 25 | issue = 2 | pages = 497–504 | date = Feb 2011 | pmid = 20923965 | doi = 10.1096/fj.10-171207 | doi-access = free | pmc = 6188353 }}</ref><ref name=Mendz>{{cite journal|last=Mendz|first=George|author2=Stuart Hazell|title=Evidence for a pentose phosphate pathway in Helicobacter pylori|journal=FEMS Microbiology Letters|year=1991|volume=84|issue=3|pages=331–336|doi=10.1111/j.1574-6968.1991.tb04619.x|doi-access=free}}</ref>   This enzyme has also been implicated in additional [[pentose]] and glucuronate interconversions.

In ''[[Cupriavidus metallidurans]]'' two copies of the gene coding for PPE are known,<ref name="PUB00002204">{{cite journal | vauthors = Kusian B, Yoo JG, Bednarski R, Bowien B | title = The Calvin cycle enzyme pentose-5-phosphate 3-epimerase is encoded within the cfx operons of the chemoautotroph Alcaligenes eutrophus | journal = Journal of Bacteriology | volume = 174 | issue = 22 | pages = 7337–44 | date = Nov 1992 | doi = 10.1128/jb.174.22.7337-7344.1992 | pmid = 1429456 | pmc = 207429 }}</ref> one is chromosomally encoded {{Uniprot|P40117}}, the other one is on a plasmid {{Uniprot|Q04539}}. PPE has been found in a wide range of bacteria, archaebacteria, fungi and plants. All the proteins have from 209 to 241 amino acid residues. The enzyme has a [[TIM barrel]] structure.

== Nomenclature ==

The [[List of enzymes|systematic name]] of this enzyme class is D-ribulose-5-phosphate 3-epimerase. Other names in common use include
{{div col|colwidth=20em}}
* phosphoribulose epimerase,
* erythrose-4-phosphate isomerase,
* phosphoketopentose 3-epimerase,
* xylulose phosphate 3-epimerase,
* phosphoketopentose epimerase,
* ribulose 5-phosphate 3-epimerase, 
* D-ribulose phosphate-3-epimerase,
* D-ribulose 5-phosphate epimerase,
* D-ribulose-5-P 3-epimerase,
* D-xylulose-5-phosphate 3-epimerase, and 
* pentose-5-phosphate 3-epimerase.
{{Div col end}}

This enzyme participates in 3 [[metabolism|metabolic pathways]]: [[pentose phosphate pathway]], [[pentose and glucuronate interconversions]], and [[carbon fixation]].

The human protein containing this domain is the [[RPE (gene)]].

== Family ==

Phosphopentose epimerase belongs to two protein families of increasing hierarchy. This enzyme belongs to the [[isomerase]] family, specifically those [[racemase]]s and [[epimerase]]s which act on [[carbohydrates]] and their derivatives.<ref name=Akana>{{cite journal | vauthors = Akana J, Fedorov AA, Fedorov E, Novak WR, Babbitt PC, Almo SC, Gerlt JA | title = D-Ribulose 5-phosphate 3-epimerase: functional and structural relationships to members of the ribulose-phosphate binding (beta/alpha)8-barrel superfamily | journal = Biochemistry | volume = 45 | issue = 8 | pages = 2493–503 | date = Feb 2006 | pmid = 16489742 | doi = 10.1021/bi052474m }}</ref>   In addition, the [[Structural Classification of Proteins database]] has defined the “ribulose phosphate binding” superfamily for which this [[epimerase]] is a member.<ref name=Akana />  Other proteins included in this superfamily are 5‘-monophosphate decarboxylase (OMPDC), and 3-keto-l-gulonate 6-phosphate decarboxylase (KGPDC).

== Structure ==

As of late 2007, 4 [[tertiary structure|structures]] have been solved for this class of enzymes, with [[Protein Data Bank|PDB]] accession codes {{PDB link|1H1Y}}, {{PDB link|1H1Z}}, {{PDB link|1RPX}}, and {{PDB link|1TQJ}}.

=== Overall ===

Crystallographic studies have helped elucidate the [[apoenzyme]] structure of phosphopentose epimerase. Results of these studies have shown that this enzyme exists as a [[homodimer]] in solution.<ref name=Chen5>{{cite journal | vauthors = Chen YR, Hartman FC, Lu TY, Larimer FW | title = D-Ribulose-5-phosphate 3-epimerase: cloning and heterologous expression of the spinach gene, and purification and characterization of the recombinant enzyme | journal = Plant Physiology | volume = 118 | issue = 1 | pages = 199–207 | date = Sep 1998 | pmid = 9733539 | pmc = 34857 | doi = 10.1104/pp.118.1.199 }}</ref><ref name=Karmali>{{cite journal | vauthors = Karmali A, Drake AF, Spencer N | title = Purification, properties and assay of D-ribulose 5-phosphate 3-epimerase from human erythrocytes | journal = The Biochemical Journal | volume = 211 | issue = 3 | pages = 617–23 | date = Jun 1983 | pmid = 6882362 | pmc = 1154406 | doi=10.1042/bj2110617}}</ref>   Furthermore, Phosphopentose epimerase folds into a (β/α)<sub>8</sub> [[triosephosphate isomerase]] (TIM) barrel that includes loops.<ref name=Liang />  The core barrel is composed of 8 parallel strands that make up the central [[beta sheet]], with [[helices]] located in between consecutive strands. The loops in this structure have been known to regulate [[substrate (biology)|substrate]] specificities. Specifically, the loop that connects [[helix]] α6 with strand β6 caps the [[active site]] upon binding of the substrate.<ref name=Liang />

As previously mentioned, Phosphopentose epimerase is a metalloenzyme. It requires a [[cofactor (biochemistry)|cofactor]] for functionality and binds one [[divalent]] metal [[cation]] per subunit.<ref name=UniProt>{{cite web|title=Ribulose-phosphate 3-epimerase|url=https://www.uniprot.org/uniprot/Q96AT9|work=UniProt|access-date=6 March 2013}}</ref>  This enzyme has been shown to use Zn<sup>2+</sup> predominantly for [[catalysis]], along with Co<sup>2+</sup> and Mn<sup>2+</sup>.<ref name=Liang />  However, human phosphopentose epimerase – which is encoded by the [[RPE (gene)|RPE]] gene - differs in that it binds Fe<sup>2+</sup> predominantly in catalysis. Fe<sup>2+</sup> is octahedrally coordinated and stabilizes the 2,3-enediolate reaction intermediate observed in the figure.<ref name=Liang />

=== Active site ===

The β6/α6 loop region interacts with the substrate and regulates access to the active site. Phe147, Gly148, and Ala149 of this region cap the active site once binding has occurred. In addition, the Fe<sup>2+</sup> ion is coordinated to His35, His70, Asp37, Asp175, and oxygens O2 and O3 of the substrate.<ref name=Liang />  The binding of substrate [[atoms]] to the [[iron]] [[cation]] helps stabilize the complex during catalysis. [[Mutagenesis]] studies have also indicated that two aspartic [[acids]] are located within the active site and help mediate catalysis through a 1,1-proton transfer reaction.<ref name=Akana />  The aspartic acids are the acid/base catalysts. Lastly, once the [[ligand]] is attached to the active site, a series of methionines (Met39, Met72, and Met141) restrict further movement through constriction.<ref name=Jelakovic>{{cite journal | vauthors = Jelakovic S, Kopriva S, Süss KH, Schulz GE | title = Structure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate 3-epimerase from rice | journal = Journal of Molecular Biology | volume = 326 | issue = 1 | pages = 127–35 | date = Feb 2003 | pmid = 12547196 | doi = 10.1016/S0022-2836(02)01374-8 }}</ref>

== Mechanism ==

[[File:Phosphoenolase Epimerase Mechanism.png|thumb|This is a mechanism by which phosphopentose epimerase converts ribulose 5-phosphate to xylulose 5-phosphate. The intermediate in 2,3-trans-enediolate.]]

Phosphopentose utilizes an acid/base type of catalytic mechanism. The reaction proceeds in such a way that trans-2,3-enediol phosphate is the intermediate.<ref name=Das>{{cite book|last=Das|first=Debajoyti|title=Biochemistry|year=1978|publisher=Academic Publishers|pages=454–460}}</ref><ref name=Davies>{{cite journal | vauthors = Davis L, Lee N, Glaser L | title = On the mechanism of the pentose phosphate epimerases | journal = The Journal of Biological Chemistry | volume = 247 | issue = 18 | pages = 5862–6 | date = Sep 1972 | doi = 10.1016/S0021-9258(19)44837-0 | pmid = 4560420 | url = http://www.jbc.org/content/247/18/5862 | doi-access = free }}</ref>  The two aspartic acids mentioned above act as proton donors and acceptors. Asp37 and Asp175 are both hydrogen bonded to the iron cation in the active site.<ref name=Liang />  When Asp37 is deprotonated, it attacks a proton on the third carbon of D-ribulose 5-phosphate, which forms the intermediate.<ref name=Berg>{{cite book|last=Berg|first=Jeremy|title=Biochemistry|year=2006|publisher=WH Freeman and Company|isbn=978-0-7167-8724-2|pages=570–580}}</ref>  In a concerted step, as Asp37 grabs a proton, the [[carbonyl]] bond on the substrate grabs a second proton from Asp175 to form a [[hydroxyl]] group. The iron complex helps stabilize any additional charges. It is C3 of D-ribulose 5-phosphate which undergoes this [[epimer]]ization, forming D-xylulose 5-phosphate.<ref name=Jelakovic/>  The mechanism is clearly demonstrated in the figure.

== Function ==

=== Calvin cycle ===

[[Electron microscopy]] experiments in plants have shown that phosphopentose epimerase localizes to the [[thylakoid]] membrane of [[chloroplasts]].<ref name=Chen4>{{cite journal | vauthors = Chen YR, Larimer FW, Serpersu EH, Hartman FC | title = Identification of a catalytic aspartyl residue of D-ribulose 5-phosphate 3-epimerase by site-directed mutagenesis | journal = The Journal of Biological Chemistry | volume = 274 | issue = 4 | pages = 2132–6 | date = Jan 1999 | pmid = 9890975 | doi = 10.1074/jbc.274.4.2132 | doi-access = free }}</ref>  This epimerase participates in the third phase of the [[Calvin cycle]], which involves the regeneration of [[ribulose 1,5-bisphosphate]]. RuBP is the acceptor of the carbon dioxide ([[CO2|CO<sub>2</sub>]]) in the first step of the pathway, which suggests that phosphopentose epimerase regulates flux through the Calvin cycle. Without the regeneration of ribulose 1,5-bisphosphate, the cycle will be unable to continue. Therefore, [[xylulose 5-phosphate]] is reversibly converted into [[ribulose 5-phosphate]] by this epimerase. Subsequently, phosphoribulose kinase converts ribulose 5-phosphate into ribulose 1,5-bisphosphate.<ref name=Berg />

=== Pentose phosphate pathway ===

The reactions of the [[pentose phosphate pathway]] (PPP) take place in the [[cytoplasm]]. Phosphopentose epimerase specifically affects the nonoxidative portion of the pathway, which involves the production of various sugars and precursors.<ref name=Liang />  This enzyme converts [[ribulose 5-phosphate]] into the appropriate epimer for the [[transketolase]] reaction, [[xylulose 5-phosphate]].<ref name=Berg />  Therefore, the reaction that occurs in the pentose phosphate pathway is exactly the reverse of the reaction which occurs in the Calvin cycle. The mechanism remains the same and involves the formation of an enediolate intermediate.
 
Due to its involvement in this pathway, phosphopentose epimerase is an important enzyme for the cellular response to oxidative stress.<ref name=Liang />  The generation of [[NADPH]] by the pentose phosphate pathway helps protect cells against [[reactive oxygen species]]. NADPH is able to reduce [[glutathione]], which detoxifies the body by producing water from hydrogen peroxide ([[H2O2|H<sub>2</sub>O<sub>2</sub>]]).<ref name=Liang />  Therefore, not only does phosphopentose epimerase alter flux through the PPP, but it also prevents buildup of peroxides.

== Evolution ==

The structures of many phosphopentose epimerase analogs have been discovered through crystallographic studies.<ref name=Now>{{cite journal | vauthors = Nowitzki U, Wyrich R, Westhoff P, Henze K, Schnarrenberger C, Martin W | title = Cloning of the amphibolic Calvin cycle/OPPP enzyme D-ribulose-5-phosphate 3-epimerase (EC 5.1.3.1) from spinach chloroplasts: functional and evolutionary aspects | journal = Plant Molecular Biology | volume = 29 | issue = 6 | pages = 1279–91 | date = Dec 1995 | doi = 10.1007/bf00020468 | pmid = 8616224 | s2cid = 4215318 }}</ref><ref name=Wise>{{cite journal | vauthors = Wise EL, Akana J, Gerlt JA, Rayment I | title = Structure of D-ribulose 5-phosphate 3-epimerase from Synechocystis to 1.6 A resolution | journal = Acta Crystallographica Section D | volume = 60 | issue = Pt 9 | pages = 1687–90 | date = Sep 2004 | pmid = 15333955 | doi = 10.1107/S0907444904015896 }}</ref>  Due to its role in the Calvin cycle and the pentose phosphate pathway, the overall structure is conserved. When the sequences of evolutionarily-distant organisms were compared, greater than 50% similarity was observed.<ref name=Teige>{{cite journal | vauthors = Teige M, Kopriva S, Bauwe H, Süss KH | title = Chloroplast pentose-5-phosphate 3-epimerase from potato: cloning, cDNA sequence, and tissue-specific enzyme accumulation | journal = FEBS Letters | volume = 377 | issue = 3 | pages = 349–52 | date = Dec 1995 | pmid = 8549753 | doi = 10.1016/0014-5793(95)01373-3 | s2cid = 34359563 | doi-access = free | bibcode = 1995FEBSL.377..349T }}</ref>  However, amino acids positioned at the [[Protein dimer|dimer]] interface – which are involved in many intermolecular interactions – are not necessarily conserved. It is important to note that the members of the “ribulose phosphate binding” superfamily resulted from [[divergent evolution]] from a (β/α)<sub>8</sub> - barrel ancestor.<ref name=Akana />

== Drug targeting and malaria ==

The [[protozoan]] [[organism]] ''[[Plasmodium falciparum]]'' is a major causative agent of [[malaria]]. Phosphopentose epimerase has been implicated in the shikimate pathway, an essential pathway for the propagation of malaria.<ref name=Car>{{cite journal | vauthors = Caruthers J, Bosch J, Buckner F, Van Voorhis W, Myler P, Worthey E, Mehlin C, Boni E, DeTitta G, Luft J, Lauricella A, Kalyuzhniy O, Anderson L, Zucker F, Soltis M, Hol WG | title = Structure of a ribulose 5-phosphate 3-epimerase from Plasmodium falciparum | journal = Proteins | volume = 62 | issue = 2 | pages = 338–42 | date = Feb 2006 | pmid = 16304640 | doi = 10.1002/prot.20764 | s2cid = 9256275 }}</ref>  As the enzyme converts ribulose 5-phosphate into xylulose 5-phosphate, the latter is further metabolized into [[erythrose 4-phosphate]]. The shikimate pathway then converts erythrose 4-phosphate into chorismate.<ref name=Car />  It is phosphopentose epimerase which allows ''Plasmodium falciparum'' to use erythorse 4-phosphate as a substrate. Due to this enzyme’s involvement in the shikimate pathway, phosphopentose epimerase is a potential drug target for developing antimalarials.

== See also ==
*[[Ribose-5-phosphate isomerase|Phosphopentose Isomerase]]
*[[Phosphoribulokinase|Phosphoribulose Kinase]]
*[[Pentose phosphate pathway|Pentose Phosphate Pathway]]
*[[TIM barrel]] 
*[[RPE (gene)|RPE]] (human gene encoding Ribulose-phosphate 3-epimerase)

== References ==
{{reflist|33em}}

==External links==
{{Commons category}}
*[https://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=stryer.figgrp.2802 Diagram at nlm.nih.gov]
*[http://cmgm.stanford.edu/biochem200/OVERHEADS_PPP.html Diagram at stanford.edu]
*[http://www.fasebj.org/content/25/2/497.long#]

{{Pentose phosphate pathway}}
{{Racemases and epimerases}}
{{Enzymes}}
{{Portal bar|Biology|border=no}}

[[Category:EC 5.1.3]]
[[Category:Enzymes of known structure]]
[[Category:Pentose phosphate pathway]]