Phosphoenolpyruvate carboxylase: Difference between revisions

Jump to navigation Jump to search
← Older edit
Karsten Theis (talk | contribs)
Macro
4,174 edits
No edit summary
Michal Harel (talk | contribs)
31,761 edits
No edit summary
 
(10 intermediate revisions by one other user not shown)
Line 3: Line 3:
'''Phosphoenolpyruvate carboxylase''' (PEPC) catalyzes  the irreversible β-carboxylation of PEP in the presence of HCO3- to yield OAA (oxaloacetate) and Pi ( inorganic phosphate), using Mg2 + as a cofactor <ref name="O'Leary2011">PMID: 21524275</ref>. It is a key element in [https://en.wikipedia.org/wiki/C4_carbon_fixation C4 carbon fixation] <ref name="sage2004">PMID: 33873498</ref>.
'''Phosphoenolpyruvate carboxylase''' (PEPC) catalyzes  the irreversible β-carboxylation of PEP in the presence of HCO3- to yield OAA (oxaloacetate) and Pi ( inorganic phosphate), using Mg2 + as a cofactor <ref name="O'Leary2011">PMID: 21524275</ref>. It is a key element in [https://en.wikipedia.org/wiki/C4_carbon_fixation C4 carbon fixation] <ref name="sage2004">PMID: 33873498</ref>.


[[Image:C4_PEPC_reaction_and_regulation.png|center|frame|caption position=bottom|'''Figure 1''' Schematic representation of PEPC catalysis of phosphoenolpyruvate carboxylation. Adapted from Svensson et al. 2003. <ref name="svensson2003"/>]]
[[Image:C4_PEPC_reaction_and_regulation.png|center|thumb|800px|caption position=bottom|'''Figure 1''' Reaction catalyzed by PEPC. In the reaction, a carbon-carbon bond is formed, resulting in a product with four carbon atoms ("C4").]]


== Overview ==
== Overview ==
[[Image:C4_photosynthesis_cycle.png|thumb|400px|caption position=bottom| '''Figure 2''' Diagrammatic representation of the C4 photosynthetic pathway as it occurs in plants of the NADP-malic enzyme (NADP-ME) subtype. Adapted from Sage et al. 2012. <ref name="sage2012"/>]]
[[Image:C4_photosynthesis_cycle.png|thumb|400px|caption position=bottom| '''Figure 2''' Diagrammatic representation of the C4 photosynthetic pathway ([https://bio.libretexts.org/Courses/Lumen_Learning/Biology_for_Non_Majors_II_%28Lumen%29/10%3A_Module_7-_Plant_Structure_and_Function/10.13%3A_Plant_Photorespiration source])]]


The enzyme phosphoenolpyruvate carboxylase (PEPC) catalyzes the carboxylation of phosphoenolpyruvate to form oxaloacetate, with Mg2+ or Mn2+ as essential cofactors <ref name="kai2003">PMID: 12781768</ref><ref name="svensson2003">PMID: 12781769</ref>. It can be considered the key enzyme in the [https://en.wikipedia.org/wiki/C4_carbon_fixation C4 photosynthesis] process, once it’s a central part of the mechanism that makes C4 plants more efficient in carbon fixation compared to classical C3-photosynthetic pathway plants, especially in abiotic stress environments  <ref name="sage2012">PMID: 22404472</ref>. PEPC is a ubiquitous enzyme, present in the genome of all plants. However, the isoforms found in C4 metabolism plants differ in their kinetic and regulatory characteristics, when compared to C3 orthologs  <ref name="Paulus2013">PMID: 23443546</ref>. Among the Flaverina genus of the [https://en.wikipedia.org/wiki/Asteraceae Asteraceae] family, closely related C3 and C4 species are found, providing a good model to study the differences  between the two processes. The comparative analysis of ''Flaverina pringlei'' (C3) and [https://en.wikipedia.org/wiki/Flaveria_trinervia ''Flaverina trinervia''] (C4) PEPC’s,  has shown that the exchange of single amino acids can be responsible for the observed differences in saturation kinetics and inhibitor tolerance between PEPC’s of C3 and C4 species <ref name="blasing2000">PMID: 10871630</ref><ref name="Paulus2013"/>.
The enzyme phosphoenolpyruvate carboxylase (PEPC) catalyzes the carboxylation of phosphoenolpyruvate to form oxaloacetate, with Mg2+ or Mn2+ as essential cofactors <ref name="kai2003">PMID: 12781768</ref><ref name="svensson2003">PMID: 12781769</ref>. It can be considered the key enzyme in the [https://en.wikipedia.org/wiki/C4_carbon_fixation C4 photosynthesis] process, once it’s a central part of the mechanism that makes C4 plants more efficient in carbon fixation compared to classical C3-photosynthetic pathway plants, especially in abiotic stress environments  <ref name="sage2012">PMID: 22404472</ref>. PEPC is a ubiquitous enzyme, present in the genome of all plants. However, the isoforms found in C4 metabolism plants differ in their kinetic and regulatory characteristics, when compared to C3 orthologs  <ref name="Paulus2013">PMID: 23443546</ref>. Among the Flaverina genus of the [https://en.wikipedia.org/wiki/Asteraceae Asteraceae] family, closely related C3 and C4 species are found, providing a good model to study the differences  between the two processes. The comparative analysis of ''Flaverina pringlei'' (C3) and [https://en.wikipedia.org/wiki/Flaveria_trinervia ''Flaverina trinervia''] (C4) PEPC’s,  has shown that the exchange of single amino acids can be responsible for the observed differences in saturation kinetics and inhibitor tolerance between PEPC’s of C3 and C4 species <ref name="blasing2000">PMID: 10871630</ref><ref name="Paulus2013"/>.
Line 17: Line 17:
Although all enzymes of the C4 cycle are present in C3 plants, there are important changes found in C4 isoforms, specially in PEPC enzymes, that make C4 metabolism possible. PEPC’s have several non-photosynthetic related functions in different plant tissues. In C4 plants, however, changes in the promotor and enzyme structures allow for strong and specific mesophyll expression, reduced sensitivity to negative feedback inhibitors and higher kinetic efficiency <ref name="blasing2000"/><ref>PMID: 12781769</ref><ref name="Paulus2013"/>. Without this characteristics, efficient carbon fixation in the mesophyll and subsequent carbon concentration in the BS wouldn’t be possible. Therefore, the evolution  of PEPC’s C4 isoforms is one of the most important steps in the establishment of the C4 pathway <ref name="sage2004"/>.
Although all enzymes of the C4 cycle are present in C3 plants, there are important changes found in C4 isoforms, specially in PEPC enzymes, that make C4 metabolism possible. PEPC’s have several non-photosynthetic related functions in different plant tissues. In C4 plants, however, changes in the promotor and enzyme structures allow for strong and specific mesophyll expression, reduced sensitivity to negative feedback inhibitors and higher kinetic efficiency <ref name="blasing2000"/><ref>PMID: 12781769</ref><ref name="Paulus2013"/>. Without this characteristics, efficient carbon fixation in the mesophyll and subsequent carbon concentration in the BS wouldn’t be possible. Therefore, the evolution  of PEPC’s C4 isoforms is one of the most important steps in the establishment of the C4 pathway <ref name="sage2004"/>.


<StructureSection load='' size='400' side='right' scene='57/573979/Tetramer/1' pspeed='8'>
<StructureSection load='' size='400' side='right' scene='57/573979/Tetramer/2' pspeed='8'>
== PEPC enzyme structure ==
== PEPC enzyme structure ==


Overall, plant PEPC’s present a similar structure characterized by four 105-110kDa  identical subunits with a conserved N-terminal serine-phosphorylation domain, forming homotetramers <ref name="kai2003"/><ref name="O'Leary2011"/>. X-ray crystallography studies on ''Escherichia coli'' and maize (''Zea mays'') PEPC’s show that the tetramer is comprised of two pairs of monomers with a greater amount of intersubunit contacts, suggesting a homotetrameric structure of a ‘‘dimer-of-dimers’’. The dimers are held together through an interaction between Arg-438 of one subunit and Glu-433 of the neighboring subunit, forming a salt bridge <ref>PMID: 9927652</ref>. The monomeric structure  maize’s C4-PEPC monomer consists of an eight-stranded β barrel and  42 α helices <ref name="kai2003"/><ref name="Izui2004">PMID: 15725057</ref>. The <scene name='57/573979/Cv/2'>active site</scene> of each monomer, bound to PEP and the <scene name='57/573979/Cv/3'>Mn+2 ion</scene> cofactor, is located in the C-terminus region of the β barrel <ref name="matsumura2002">PMID: 12467579</ref>.
Overall, plant PEPC’s present a similar structure characterized by four 105-110kDa  identical subunits with a conserved N-terminal serine-phosphorylation domain, forming homotetramers <ref name="kai2003"/><ref name="O'Leary2011"/>. X-ray crystallography studies on ''Escherichia coli'' and maize (''Zea mays'') PEPC’s show that the tetramer is comprised of two pairs of monomers with a greater amount of intersubunit contacts, suggesting a homotetrameric structure of a ‘‘dimer-of-dimers’’. The dimers are held together through an interaction between Arg-438 of one subunit and Glu-433 of the neighboring subunit, forming a salt bridge <ref>PMID: 9927652</ref>. The monomeric structure  maize’s C4-PEPC monomer consists of an eight-stranded β barrel and  42 α helices <ref name="kai2003"/><ref name="Izui2004">PMID: 15725057</ref>. The <scene name='57/573979/Cv/3'>active site</scene> of each monomer, bound to PEP and the <scene name='57/573979/Cv/3'>Mn+2 ion</scene> cofactor, is located in the C-terminus region of the β barrel <ref name="matsumura2002">PMID: 12467579</ref>.


[[Image:4BXC_F.trinervia_PEPC+G6P_crystral_structure.png|center|frame|caption position=bottom|'''Figure 3''' X-ray crystal structure of ''Flaverina trinervia’s'' C4 PEPC bound to glucose 6-phosphate (magenta). Two strongly bound dimers (left and right sides of the structure) form the tetrameric quaternary structure. Adapted from Schlieper et al. 2014. <ref name="schlieper2014">PMID: 24043710</ref>]]  
[[Image:4BXC_F.trinervia_PEPC+G6P_crystral_structure.png|center|frame|caption position=bottom|'''Figure 3''' X-ray crystal structure of ''Flaverina trinervia’s'' C4 PEPC bound to glucose 6-phosphate (magenta). Two strongly bound dimers (left and right sides of the structure) form the tetrameric quaternary structure. Adapted from Schlieper et al. 2014. <ref name="schlieper2014">PMID: 24043710</ref>]]  
Line 29: Line 29:
== Allosteric regulation and reaction mechanism ==
== Allosteric regulation and reaction mechanism ==


PEPC’s carboxylase activity is regulated by different post-translational mechanisms. In C4 and CAM plants, the phosphorylation of a serine residue near the N terminus (S15 in maize C4-PEPC) activates the enzyme by decreasing its sensitivity to allosteric inhibitors such as aspartate and malate and increasing activation by the positive allosteric regulator glucose 6-phosphate <ref name="O'Leary2011"/>. Studies on'' F. pringlei'' and ''F. trinervia'', have positively identified the residues Arg641, Lys829, Arg888 and Asn964 as binding motif of the negative allosteric inhibitors aspartate and malate <ref name="Paulus2013"/>. Similar studies have also identified the <scene name='57/573979/Cv/5'>aspartate binding site</scene> site in maize <ref name="matsumura2002"/>. In C3 PEPC, Arg884 provides an additional hydrogen bond for inhibitor binding, whereas in C4 PEPC isoforms the substitution of this residue by a glycine, reducing the enzymes sensitivity towards both feedback inhibitors <ref>PMID: 21491491</ref><ref name="Paulus2013"/>. The positive allosteric effector glucose 6-phosphate’s binding site has also been identified in the C4-PEPC of maize. X-ray crystallography of maize’s C4-PEPC in complex with sulfate ion (a positive effector analog of  glucose 6-phosphate) revealed that the positive effector was bound to the enzyme at the dimer interface and was surrounded by four positively charged residues (R183, R184, R231, and R372 in the adjacent subunit <ref name="kai2003"/>.
PEPC’s carboxylase activity is regulated by different post-translational mechanisms. In C4 and CAM plants, the phosphorylation of a serine residue near the N terminus (S15 in maize C4-PEPC) activates the enzyme by decreasing its sensitivity to allosteric inhibitors such as aspartate and malate and increasing activation by the positive allosteric regulator glucose 6-phosphate <ref name="O'Leary2011"/>. Studies on'' F. pringlei'' and ''F. trinervia'', have positively identified the residues Arg641, Lys829, Arg888 and Asn964 as binding motif of the negative allosteric inhibitors aspartate and malate <ref name="Paulus2013"/>. Similar studies have also identified the <scene name='57/573979/Cv/8'>aspartate binding site</scene> site in maize <ref name="matsumura2002"/>. In C3 PEPC, Arg884 provides an additional hydrogen bond for inhibitor binding, whereas in C4 PEPC isoforms the substitution of this residue by a glycine, reducing the enzymes sensitivity towards both feedback inhibitors <ref>PMID: 21491491</ref><ref name="Paulus2013"/>. The positive allosteric effector glucose 6-phosphate’s binding site has also been identified in the C4-PEPC of maize. X-ray crystallography of maize’s C4-PEPC in complex with sulfate ion (a positive effector analog of  glucose 6-phosphate) revealed that the positive effector was bound to the enzyme at the dimer interface and was surrounded by four positively charged residues (R183, R184, R231, and R372 in the adjacent subunit <ref name="kai2003"/>.


[[Image:Inhibitor-binding_site_of_Flaverina_trinervia_C4_PEPC.png|center|frame|caption position=bottom|'''Figure 4''' Inhibitor-binding site of ''Flaverina trinervia’s'' C4 PEPC. Adapted from Paulus et al. 2013. <ref name="Paulus2013"/>]]
[[Image:Inhibitor-binding_site_of_Flaverina_trinervia_C4_PEPC.png|center|frame|caption position=bottom|'''Figure 4''' Inhibitor-binding site of ''Flaverina trinervia’s'' C4 PEPC. Adapted from Paulus et al. 2013. <ref name="Paulus2013"/>]]
Line 37: Line 37:
Most proposed catalytic reaction mechanisms suggest that PEPC catalyzes an ordered multistep reaction in which the preferred order of reactant binding to the active site are: first the bivalent cation ( Mg2+ or Mn2+), then PEP and lastly bicarbonate (HCO3- ) <ref name="kai2003"/><ref name="Izui2004"/>. In a review article on the subject, Izui et al., 2004 <ref name="Izui2004"/>, proposes a detailed reaction mechanism for the enzyme, based on maize and'' E.coli'' PEPC structures in which PEP is located in a hydrophobic pocket consisting of W248, L504, and M538 residues. In this model, H177 is a critically important catalytic base as it is supposed to play a role in stabilizing the carboxyphosphate intermediate and abstracting a proton from its carboxyl group.
Most proposed catalytic reaction mechanisms suggest that PEPC catalyzes an ordered multistep reaction in which the preferred order of reactant binding to the active site are: first the bivalent cation ( Mg2+ or Mn2+), then PEP and lastly bicarbonate (HCO3- ) <ref name="kai2003"/><ref name="Izui2004"/>. In a review article on the subject, Izui et al., 2004 <ref name="Izui2004"/>, proposes a detailed reaction mechanism for the enzyme, based on maize and'' E.coli'' PEPC structures in which PEP is located in a hydrophobic pocket consisting of W248, L504, and M538 residues. In this model, H177 is a critically important catalytic base as it is supposed to play a role in stabilizing the carboxyphosphate intermediate and abstracting a proton from its carboxyl group.


[[Image:PEPC reaction mechanism.png|center|frame|caption position=bottom|'''Figure 5''' Catalytic mechanism of PEPC based on maize C4-PEPC and ''E. coli'' PEPC crystal structures and the three-step reaction model. The hydrophobic pocket is shown as yellow circles and the residues show maize numbering. Adapted from Izui et al. 2004. <ref name="Izui2004"/>]]
[[Image:PEPC reaction mechanism.png|center|thumb|600 px|caption position=bottom|'''Figure 5''' Catalytic mechanism of PEPC based on maize C4-PEPC and ''E. coli'' PEPC crystal structures and the three-step reaction model. The hydrophobic pocket is shown as yellow circles and the residues show maize numbering. Adapted from Izui et al. 2004. <ref name="Izui2004"/>]]


</StructureSection>
</StructureSection>
Line 60: Line 60:


'''''Arabidopsis thaliana'''''<br>
'''''Arabidopsis thaliana'''''<br>
[[5fdn]] – AtPEPC 3 + aspartate + citrate<br>
[[8oj9]] – AtPEPC 1  <br />
[[8ojf]] – AtPEPC 1 + phosphate <br />
[[8oje]] – AtPEPC 1 + malate <br />
[[5fdn]] – AtPEPC 3 + aspartate + citrate <br />


'''''Flaveria pringlei'''''<br>
'''''Flaveria pringlei'''''<br>

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman, Lucas Xavier da Cunha, Karsten Theis
Retrieved from "https://proteopedia.openfox.io/w/Phosphoenolpyruvate_carboxylase"