Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015
Pathway Tools
Intro Tutorial
discounted registration ends Sept 5, 2015

Escherichia coli K-12 substr. MG1655 Enzyme: 1-deoxy-D-xylulose 5-phosphate reductoisomerase

Gene: dxr Accession Numbers: EG12715 (EcoCyc), b0173, ECK0172

Synonyms: yaeM, ispC

Regulation Summary Diagram: ?

Regulation summary diagram for dxr

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 [Kuzuyama00]. 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 [Li13, 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 [Kuzuyama00].

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].

Locations: cytosol

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

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0019288 - isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway Inferred from experiment Inferred by computational analysis [UniProtGOA12, Altincicek01b]
GO:0008299 - isoprenoid biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016114 - terpenoid biosynthetic process Inferred by computational analysis [GOA06]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0030145 - manganese ion binding Inferred from experiment [Takahashi98]
GO:0030604 - 1-deoxy-D-xylulose-5-phosphate reductoisomerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Kuzuyama00]
GO:0042802 - identical protein binding Inferred from experiment [Takahashi98]
GO:0046872 - metal ion binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA01a, Takahashi98]
GO:0070402 - NADPH binding Inferred from experiment Inferred by computational analysis [GOA01a, Takahashi98]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers menaquinone, ubiquinone

Essentiality data for dxr knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Curated 27-Apr-2007 by Shearer A , SRI International
Last-Curated ? 16-Aug-2013 by Kubo A , SRI International

Enzymatic reaction of: 1-deoxy-D-xylulose 5-phosphate reductoisomerase

Synonyms: 2C-methyl-D-erythritol 4-phosphate synthase, MEP synthase, DXP reductoisomerase

EC Number:

2-C-methyl-D-erythritol 4-phosphate + NADP+ <=> 1-deoxy-D-xylulose 5-phosphate + NADPH + H+

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 [Kuzuyama00]. 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].

Cofactors or Prosthetic Groups: NADPH [Kuzuyama00], Mn2+ [Mac05, Kuzuyama00, Takahashi98]

Alternative Cofactors for Mn2+: Co2+ , Mg2+

Inhibitors (Unknown Mechanism): fosmidomycin [Kuzuyama00, NguyenTrung13]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Fox05a, BRENDA14]
7.0, 9.0, 20.0, 7.4
[Kuzuyama00, BRENDA14]
1-deoxy-D-xylulose 5-phosphate
[Wong07, BRENDA14]
1-deoxy-D-xylulose 5-phosphate
60.0, 99.0, 250.0
[Kuzuyama00, BRENDA14]
1-deoxy-D-xylulose 5-phosphate
[Wong04, BRENDA14]
1-deoxy-D-xylulose 5-phosphate
73.0, 97.0
[Hoeffler02, BRENDA14]
1-deoxy-D-xylulose 5-phosphate
1-deoxy-D-xylulose 5-phosphate
[Fox05a, BRENDA14]
1-deoxy-D-xylulose 5-phosphate
[Walker05, BRENDA14]
1-deoxy-D-xylulose 5-phosphate
[Fox05, BRENDA14]

T(opt): 50 °C [BRENDA14, Kuzuyama00]

pH(opt): 7 [BRENDA14, Kuzuyama00], 7.5 [BRENDA14, Takahashi98], 7-8.5 [Kuzuyama00]

Sequence Features

Protein sequence of Dxr with features indicated

Feature Class Location Attached Group Citations Comment
Nucleotide-Phosphate-Binding-Region 7 -> 36 NADP+
[Mac05, Yajima02, UniProt15]
UniProt: NADP.
Mutagenesis-Variant 14  
[Kuzuyama00, UniProt11a]
UniProt: Loss of solubility and activity.
Amino-Acid-Sites-That-Bind 125  
[Mac05, UniProt15]
UniProt: Substrate.
Metal-Binding-Site 150  
UniProt: Divalent metal cation.
Metal-Binding-Site 152  
[Mac05, UniProt15]
UniProt: Divalent metal cation.
Mutagenesis-Variant 153  
[Kuzuyama00, UniProt11a]
UniProt: Increase in KM for substrate. Reduces activity 35-fold.
Amino-Acid-Sites-That-Bind 186  
[Mac05, UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 209  
[Mac05, UniProt15]
UniProt: Substrate.
Mutagenesis-Variant 209  
[Kuzuyama00, UniProt11a]
UniProt: Increase in KM for substrate. Reduces activity 5000-fold.
Protein-Segment 222 -> 228  
UniProt: Binding to substrate phosphate group; Sequence Annotation Type: region of interest;
Metal-Binding-Site 231  
[Mac05, UniProt15]
UniProt: Divalent metal cation.
Mutagenesis-Variant 231  
[Kuzuyama00, UniProt11a]
UniProt: No effect on KM for substrate. Reduces activity by over 99.9%.
Mutagenesis-Variant 257  
[Kuzuyama00, UniProt11a]
UniProt: Strong increase in KM for substrate. Loss of activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b0173 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12715; confirmed by SwissProt match.


Altincicek01b: 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

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014."

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

Cheng04: Cheng F, Oldfield E (2004). "Inhibition of isoprene biosynthesis pathway enzymes by phosphonates, bisphosphonates, and diphosphates." J Med Chem 47(21);5149-58. PMID: 15456258

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

Fox05a: Fox DT, Poulter CD (2005). "Mechanistic studies with 2-C-methyl-D-erythritol 4-phosphate synthase from Escherichia coli." Biochemistry 44(23);8360-8. PMID: 15938625

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

Kuzuyama00: 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

Li13: 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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

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

Wong07: Wong U, Cox RJ (2007). "The chemical mechanism of D-1-deoxyxylulose-5-phosphate reductoisomerase from Escherichia coli." Angew Chem Int Ed Engl 46(26);4926-9. PMID: 17516600

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

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Tue Sep 1, 2015, biocyc11.