|Gene:||dxr||Accession Numbers: EG12715 (EcoCyc), b0173, ECK0172|
Synonyms: yaeM, ispC
Subunit composition of 1-deoxy-D-xylulose 5-phosphate reductoisomerase = [Dxr]2
1-deoxy-D-xylulose 5-phosphate reductoisomerase (Dxr) is involved in the first committed step in the methylerythritol phosphate pathway of isoprenoid biosynthesis. Dxr catalyzes the conversion of 1-deoxy-D-xylulose 5-phosphate (DXP) into the dedicated MEP pathway intermediate 2-C-methyl-D-erythritol-4-phosphate (MEP). This reaction is NADPH-dependent, and required a bivalent metal cofactor [Takahashi98]. This is a two-step reaction. The first step is a non-reductive, NADPH-dependent rearrangement that generates MEP. This is followed by an NADPH-dependent reduction of this intermediate to generate the final product [Hoeffler02].
This reaction appears to depend on one or more of Dxr's histidines [Kuzuyama00a]. Based on the stereospecificity of the reaction, Dxr is a class B dehydrogenase [Radykewicz00]. Different mechanisms for the DXR catalyzed reaction have been proposed and investigated [Li13b, Fox05a, Munos09].
A number of structures have been determined for Dxr. A crystal structure of the dimer to 2.5 Å resolution shows that the Dxr connective domain is responsible for dimerization and contains the bulk of the enzyme's active site [Reuter02]. A crystal structure of Dxr complexed with NADPH and a sulfur ion to 2.2 Å resolution shows that a flexible loop covers the active site [Yajima02]. Crystal structures of Dxr both unbound and bound to the inhibitor and antimalarial drug fosmidomycin show that drug binding causes a substantial conformational change [Steinbacher03, Mac05]. Crystal structures of Dxr bound to bisphonates indicate that these compounds bind the same site as fosmidomycin [Yajima04].
dxr deficient mutants required 2-C-methylerythritol, a free alcohol for MEP, for growth and survival [Takahashi98]. Analysis of dxr-deficient mutants identified Glu231 to play an important role in the conversion of DXP to MEP [Kuzuyama00a].
Since the enzymes of the methylerythritol pathway are not found in humans, these enzymes, especially DXR, have attracted much interest for its potential as anti-infective drug targets. New classes of inhibitors have been extensively studied. [NguyenTrung13, Cai12, Zingle12, Jackson12] Both computational and high-throughput experimental methods have been used to attempt to identify inhibitors of Dxr [Gottlin03, Cheng04, Merckle05].
Dxr is required for cell survival [Kuzuyama99].
|Map Position: [193,521 -> 194,717] (4.17 centisomes, 15°)||Length: 1197 bp / 398 aa|
Molecular Weight of Polypeptide: 43.388 kD (from nucleotide sequence), 42.0 kD (experimental) [Takahashi98 ]
Unification Links: ASAP:ABE-0000592 , DIP:DIP-9484N , EchoBASE:EB2575 , EcoGene:EG12715 , EcoliWiki:b0173 , ModBase:P45568 , OU-Microarray:b0173 , PortEco:dxr , PR:PRO_000022494 , Pride:P45568 , Protein Model Portal:P45568 , RefSeq:NP_414715 , RegulonDB:EG12715 , SMR:P45568 , String:511145.b0173 , UniProt:P45568
Relationship Links: InterPro:IN-FAMILY:IPR003821 , InterPro:IN-FAMILY:IPR013512 , InterPro:IN-FAMILY:IPR013644 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR026877 , Panther:IN-FAMILY:PTHR30525 , PDB:Structure:1JVS , PDB:Structure:1K5H , PDB:Structure:1ONN , PDB:Structure:1ONO , PDB:Structure:1ONP , PDB:Structure:1Q0H , PDB:Structure:1Q0L , PDB:Structure:1Q0Q , PDB:Structure:1T1R , PDB:Structure:1T1S , PDB:Structure:2EGH , PDB:Structure:3ANL , PDB:Structure:3ANM , PDB:Structure:3ANN , PDB:Structure:3R0I , Pfam:IN-FAMILY:PF02670 , Pfam:IN-FAMILY:PF08436 , Pfam:IN-FAMILY:PF13288
|Biological Process:||GO:0019288 - isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
GO:0008299 - isoprenoid biosynthetic process [UniProtGOA11a, GOA01a]
GO:0016114 - terpenoid biosynthetic process [GOA06]
GO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
|Molecular Function:||GO:0030145 - manganese ion binding
GO:0030604 - 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity [GOA06, GOA01, GOA01a, Kuzuyama00a]
GO:0042802 - identical protein binding [Takahashi98]
GO:0046872 - metal ion binding [UniProtGOA11a, GOA01a, Takahashi98]
GO:0070402 - NADPH binding [GOA01a, Takahashi98]
GO:0016491 - oxidoreductase activity [UniProtGOA11a]
|Cellular Component:||GO:0005829 - cytosol [DiazMejia09]|
|MultiFun Terms:||metabolism → biosynthesis of building blocks → cofactors, small molecule carriers → menaquinone, ubiquinone|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB Lennox||No||37||Aerobic||7||No [Baba06, Comment 1]|
Enzymatic reaction of: 1-deoxy-D-xylulose 5-phosphate reductoisomerase
Synonyms: 2C-methyl-D-erythritol 4-phosphate synthase, MEP synthase, DXP reductoisomerase
EC Number: 220.127.116.117
The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.
This reaction is reversible. [Hoeffler02]
In Pathways: methylerythritol phosphate pathway I
Quite a few kinetic values have been determined for Dxr, at various pH values and with varying cofactors. One analysis gives Km values of 250 µM for 1-deoxy-D-xylylose 5-phosphate (DXP) and 7.4 µM for NADPH when Mn2+ is the cofactor. When Mg2+ is the cofactor, these values are 99 µM and 18 µM, respectively. When Co2+ is the cofactor, these values are 60 µM and 8.8 µM, respectively [Kuzuyama00a]. At pH 7.8, the Km for DXP also varies by cofactor, with values of 17 µM for Mn2+, 210 µM for Mg2+, and 2 µM for Co2+. At pH 6.0, the values are 520 µM for Mn2+ and 17mM for Co2+ [Mac05]. Under saturating NADPH conditions, a Km of 54 µM for DXP is reported [Fox05a].
Although this reaction is reversible, the production of 2-C-methyl-D-erythritol-4-phosphate is heavily favored in vivo [Hoeffler02].
|Feature Class||Location||Attached Group||Citations||Comment|
|Nucleotide-Phosphate-Binding-Region||7 -> 36||NADP+|
|Protein-Segment||222 -> 228|
10/20/97 Gene b0173 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12715; confirmed by SwissProt match.
Altincicek01: Altincicek B, Kollas AK, Sanderbrand S, Wiesner J, Hintz M, Beck E, Jomaa H (2001). "GcpE is involved in the 2-C-methyl-D-erythritol 4-phosphate pathway of isoprenoid biosynthesis in Escherichia coli." J Bacteriol 183(8);2411-6. PMID: 11274098
Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554
Cai12: Cai G, Deng L, Fryszczyn BG, Brown NG, Liu Z, Jiang H, Palzkill T, Song Y (2012). "Thermodynamic Investigation of Inhibitor Binding to 1-Deoxy-D-Xylulose-5-Phosphate Reductoisomerase." ACS Med Chem Lett 3(6);496-500. PMID: 23050057
DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114
Fox05: Fox DT, Poulter CD (2005). "Synthesis and evaluation of 1-deoxy-D-xylulose 5-phosphoric acid analogues as alternate substrates for methylerythritol phosphate synthase." J Org Chem 70(6);1978-85. PMID: 15760175
Gottlin03: Gottlin EB, Benson RE, Conary S, Antonio B, Duke K, Payne ES, Ashraf SS, Christensen DJ (2003). "High-throughput screen for inhibitors of 1-deoxy-d-xylulose 5-phosphate reductoisomerase by surrogate ligand competition." J Biomol Screen 8(3);332-9. PMID: 12857387
Hoeffler02: Hoeffler JF, Tritsch D, Grosdemange-Billiard C, Rohmer M (2002). "Isoprenoid biosynthesis via the methylerythritol phosphate pathway. Mechanistic investigations of the 1-deoxy-D-xylulose 5-phosphate reductoisomerase." Eur J Biochem 269(18);4446-57. PMID: 12230556
Jackson12: Jackson ER, Dowd CS (2012). "Inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase (Dxr): a review of the synthesis and biological evaluation of recent inhibitors." Curr Top Med Chem 12(7);706-28. PMID: 22283814
Kuzuyama00a: Kuzuyama T, Takahashi S, Takagi M, Seto H (2000). "Characterization of 1-deoxy-D-xylulose 5-phosphate reductoisomerase, an enzyme involved in isopentenyl diphosphate biosynthesis, and identification of its catalytic amino acid residues." J Biol Chem 2000;275(26);19928-32. PMID: 10787409
Kuzuyama99: Kuzuyama T, Takahashi S, Seto H (1999). "Construction and characterization of Escherichia coli disruptants defective in the yaeM gene." Biosci Biotechnol Biochem 63(4);776-8. PMID: 10361694
Li13b: Li H, Tian J, Sun W, Qin W, Gao WY (2013). "Mechanistic insights into 1-deoxy-D-xylulose 5-phosphate reductoisomerase, a key enzyme of the MEP terpenoid biosynthetic pathway." FEBS J. PMID: 24010408
Mac05: Mac Sweeney A, Lange R, Fernandes RP, Schulz H, Dale GE, Douangamath A, Proteau PJ, Oefner C (2005). "The crystal structure of E.coli 1-deoxy-D-xylulose-5-phosphate reductoisomerase in a ternary complex with the antimalarial compound fosmidomycin and NADPH reveals a tight-binding closed enzyme conformation." J Mol Biol 345(1);115-27. PMID: 15567415
Merckle05: Merckle L, de Andres-Gomez A, Dick B, Cox RJ, Godfrey CR (2005). "A fragment-based approach to understanding inhibition of 1-deoxy-D-xylulose-5-phosphate reductoisomerase." Chembiochem 6(10);1866-74. PMID: 16116659
Munos09: Munos JW, Pu X, Mansoorabadi SO, Kim HJ, Liu HW (2009). "A secondary kinetic isotope effect study of the 1-deoxy-D-xylulose-5-phosphate reductoisomerase-catalyzed reaction: evidence for a retroaldol-aldol rearrangement." J Am Chem Soc 131(6);2048-9. PMID: 19159292
NguyenTrung13: Nguyen-Trung AT, Tritsch D, Grosdemange-Billiard C, Rohmer M (2013). "Synthesis of tetrazole analogues of phosphonohydroxamic acids: an attempt to improve the inhibitory activity against the DXR." Bioorg Med Chem Lett 23(6);1643-7. PMID: 23414808
Radykewicz00: Radykewicz T, Rohdich F, Wungsintaweekul J, Herz S, Kis K, Eisenreich W, Bacher A, Zenk MH, Arigoni D (2000). "Biosynthesis of terpenoids: 1-deoxy-D-xylulose-5-phosphate reductoisomerase from Escherichia coli is a class B dehydrogenase." FEBS Lett 2000;465(2-3);157-60. PMID: 10631325
Reuter02: Reuter K, Sanderbrand S, Jomaa H, Wiesner J, Steinbrecher I, Beck E, Hintz M, Klebe G, Stubbs MT (2002). "Crystal structure of 1-deoxy-D-xylulose-5-phosphate reductoisomerase, a crucial enzyme in the non-mevalonate pathway of isoprenoid biosynthesis." J Biol Chem 277(7);5378-84. PMID: 11741911
Steinbacher03: Steinbacher S, Kaiser J, Eisenreich W, Huber R, Bacher A, Rohdich F (2003). "Structural basis of fosmidomycin action revealed by the complex with 2-C-methyl-D-erythritol 4-phosphate synthase (IspC). Implications for the catalytic mechanism and anti-malaria drug development." J Biol Chem 278(20);18401-7. PMID: 12621040
Takahashi98: Takahashi S, Kuzuyama T, Watanabe H, Seto H (1998). "A 1-deoxy-D-xylulose 5-phosphate reductoisomerase catalyzing the formation of 2-C-methyl-D-erythritol 4-phosphate in an alternative nonmevalonate pathway for terpenoid biosynthesis." Proc Natl Acad Sci U S A 1998;95(17);9879-84. PMID: 9707569
Walker05: Walker JR, Poulter CD (2005). "Synthesis and evaluation of 1-deoxy-D-xylulose 5-phosphate analogues as chelation-based inhibitors of methylerythritol phosphate synthase." J Org Chem 70(24);9955-9. PMID: 16292827
Wong04: Wong A, Munos JW, Devasthali V, Johnson KA, Liu HW (2004). "Study of 1-deoxy-D-xylulose-5-phosphate reductoisomerase: synthesis and evaluation of fluorinated substrate analogues." Org Lett 6(20);3625-8. PMID: 15387564
Yajima02: Yajima S, Nonaka T, Kuzuyama T, Seto H, Ohsawa K (2002). "Crystal structure of 1-deoxy-D-xylulose 5-phosphate reductoisomerase complexed with cofactors: implications of a flexible loop movement upon substrate binding." J Biochem (Tokyo) 131(3);313-7. PMID: 11872159
Yajima04: Yajima S, Hara K, Sanders JM, Yin F, Ohsawa K, Wiesner J, Jomaa H, Oldfield E (2004). "Crystallographic structures of two bisphosphonate:1-deoxyxylulose-5-phosphate reductoisomerase complexes." J Am Chem Soc 126(35);10824-5. PMID: 15339150
Zingle12: Zingle C, Kuntz L, Tritsch D, Grosdemange-Billiard C, Rohmer M (2012). "Modifications around the hydroxamic acid chelating group of fosmidomycin, an inhibitor of the metalloenzyme 1-deoxyxylulose 5-phosphate reductoisomerase (DXR)." Bioorg Med Chem Lett 22(21);6563-7. PMID: 23025997
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