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Feedback inhibition of deoxy-D-xylulose-5-phosphate synthase regulates the methylerythritol 4-phosphate pathway.
J Biol Chem. 2013 Jun 07; 288(23):16926-16936.JB

Abstract

The 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway leads to the biosynthesis of isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), the precursors for isoprene and higher isoprenoids. Isoprene has significant effects on atmospheric chemistry, whereas other isoprenoids have diverse roles ranging from various biological processes to applications in commercial uses. Understanding the metabolic regulation of the MEP pathway is important considering the numerous applications of this pathway. The 1-deoxy-D-xylulose-5-phosphate synthase (DXS) enzyme was cloned from Populus trichocarpa, and the recombinant protein (PtDXS) was purified from Escherichia coli. The steady-state kinetic parameters were measured by a coupled enzyme assay. An LC-MS/MS-based assay involving the direct quantification of the end product of the enzymatic reaction, 1-deoxy-D-xylulose 5-phosphate (DXP), was developed. The effect of different metabolites of the MEP pathway on PtDXS activity was tested. PtDXS was inhibited by IDP and DMADP. Both of these metabolites compete with thiamine pyrophosphate for binding with the enzyme. An atomic structural model of PtDXS in complex with thiamine pyrophosphate and Mg(2+) was built by homology modeling and refined by molecular dynamics simulations. The refined structure was used to model the binding of IDP and DMADP and indicated that IDP and DMADP might bind with the enzyme in a manner very similar to the binding of thiamine pyrophosphate. The feedback inhibition of PtDXS by IDP and DMADP constitutes an important mechanism of metabolic regulation of the MEP pathway and indicates that thiamine pyrophosphate-dependent enzymes may often be affected by IDP and DMADP.

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Authors+Show Affiliations

Banerjee A
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
Wu Y
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
Banerjee R
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
Li Y
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824.
Yan H
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824. Electronic address: yanh@msu.edu.
Sharkey TD
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824. Electronic address: tsharkey@msu.edu.

MeSH

ErythritolEscherichia coliHemiterpenesKineticsModels, MolecularOrganophosphorus CompoundsPlant ProteinsPopulusProtein BindingRecombinant ProteinsSugar PhosphatesThiamine PyrophosphateTransferases

Pub Type(s)

Journal Article
Research Support, U.S. Gov't, Non-P.H.S.

Language

eng

PubMed ID

23612965

Citation

Banerjee, Aparajita, et al. "Feedback Inhibition of deoxy-D-xylulose-5-phosphate Synthase Regulates the Methylerythritol 4-phosphate Pathway." The Journal of Biological Chemistry, vol. 288, no. 23, 2013, pp. 16926-16936.
Banerjee A, Wu Y, Banerjee R, et al. Feedback inhibition of deoxy-D-xylulose-5-phosphate synthase regulates the methylerythritol 4-phosphate pathway. J Biol Chem. 2013;288(23):16926-16936.
Banerjee, A., Wu, Y., Banerjee, R., Li, Y., Yan, H., & Sharkey, T. D. (2013). Feedback inhibition of deoxy-D-xylulose-5-phosphate synthase regulates the methylerythritol 4-phosphate pathway. The Journal of Biological Chemistry, 288(23), 16926-16936. https://doi.org/10.1074/jbc.M113.464636
Banerjee A, et al. Feedback Inhibition of deoxy-D-xylulose-5-phosphate Synthase Regulates the Methylerythritol 4-phosphate Pathway. J Biol Chem. 2013 Jun 7;288(23):16926-16936. PubMed PMID: 23612965.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Feedback inhibition of deoxy-D-xylulose-5-phosphate synthase regulates the methylerythritol 4-phosphate pathway. AU - Banerjee,Aparajita, AU - Wu,Yan, AU - Banerjee,Rahul, AU - Li,Yue, AU - Yan,Honggao, AU - Sharkey,Thomas D, Y1 - 2013/04/23/ PY - 2013/4/25/entrez PY - 2013/4/25/pubmed PY - 2013/8/13/medline KW - Deoxyxylulose-5-phosphate Synthase KW - Enzyme Inhibitors KW - Enzyme Structure KW - Isoprene KW - Isoprenoid KW - Methylerythritol Pathway KW - Plant Biochemistry KW - Thiamine KW - Thiamine Diphosphate SP - 16926 EP - 16936 JF - The Journal of biological chemistry JO - J Biol Chem VL - 288 IS - 23 N2 - The 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway leads to the biosynthesis of isopentenyl diphosphate (IDP) and dimethylallyl diphosphate (DMADP), the precursors for isoprene and higher isoprenoids. Isoprene has significant effects on atmospheric chemistry, whereas other isoprenoids have diverse roles ranging from various biological processes to applications in commercial uses. Understanding the metabolic regulation of the MEP pathway is important considering the numerous applications of this pathway. The 1-deoxy-D-xylulose-5-phosphate synthase (DXS) enzyme was cloned from Populus trichocarpa, and the recombinant protein (PtDXS) was purified from Escherichia coli. The steady-state kinetic parameters were measured by a coupled enzyme assay. An LC-MS/MS-based assay involving the direct quantification of the end product of the enzymatic reaction, 1-deoxy-D-xylulose 5-phosphate (DXP), was developed. The effect of different metabolites of the MEP pathway on PtDXS activity was tested. PtDXS was inhibited by IDP and DMADP. Both of these metabolites compete with thiamine pyrophosphate for binding with the enzyme. An atomic structural model of PtDXS in complex with thiamine pyrophosphate and Mg(2+) was built by homology modeling and refined by molecular dynamics simulations. The refined structure was used to model the binding of IDP and DMADP and indicated that IDP and DMADP might bind with the enzyme in a manner very similar to the binding of thiamine pyrophosphate. The feedback inhibition of PtDXS by IDP and DMADP constitutes an important mechanism of metabolic regulation of the MEP pathway and indicates that thiamine pyrophosphate-dependent enzymes may often be affected by IDP and DMADP. SN - 1083-351X UR - https://www.unboundmedicine.com/medline/citation/23612965/Feedback_inhibition_of_deoxy_D_xylulose_5_phosphate_synthase_regulates_the_methylerythritol_4_phosphate_pathway_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S0021-9258(20)53698-3 DB - PRIME DP - Unbound Medicine ER -