Escherichia coli K-12 substr. MG1655 Enzyme: IMP dehydrogenase

Gene: guaB Accession Numbers: EG10421 (EcoCyc), b2508, ECK2504

Synonyms: guaR

Regulation Summary Diagram: ?

Regulation summary diagram for guaB

Subunit composition of IMP dehydrogenase = [GuaB]4

IMP dehydrogenase catalyzes the oxidation of IMP to XMP using NAD+ as cofactor. This is the first committed, rate-limiting step in de novo guanine nucleotide biosynthesis in most organisms. Its importance has made it an enzyme of interest for the development of inhibitors (reviewed in [Hedstrom09]).

IMP dehydrogenase (IMPDH) is a homotetramer in both E. coli [Gilbert79] and humans [Nimmesgern99].

IMPDH appears to bind single-stranded nucleic acids both in vivo and in vitro [McLean04], which was shown by Kozhevnikova et al. (2012) by using purified proteins [Kozhevnikova12]. IMPDH binds efficiently to the CT-rich elements in a sequence-specific manner, and this ability is conserved from bacteria to higher eukaryotes [Kozhevnikova12].

Alanine mutagenesis studies have identified functionally important residues. A transition state analog, mizoribine 5'-monophosphate, was also identified [Kerr97]. The IMP dehydrogenase reaction was found to proceed through formation of an enzyme-XMP* intermediate involving a covalent adduct at an active site cysteine. This intermediate is then hydrolyzed to produce XMP. An Asp338Ala mutant showed that Asp338 controls hydride transfer [Kerr00]. An evolutionarily conserved cystathionine-β-synthase (CBS) subdomain (Bateman domain) in this enzyme was shown to have a role in the regulation of purine nucleotide metabolism [Pimkin08]. The Bateman domain was subsequently concluded to be a negative trans-regulator of adenylate nucleotide synthesis, independent of its catalytic role in the de novo synthesis of GMP [Pimkin09].

Gene Citations: [TesfaSelase92, Lambden73, Vales79, Shimada76, Hutchings00]

Locations: cytosol

Map Position: [2,630,626 <- 2,632,092] (56.7 centisomes, 204°)
Length: 1467 bp / 488 aa

Molecular Weight of Polypeptide: 52.022 kD (from nucleotide sequence), 58 kD (experimental) [Gilbert79 ]

Molecular Weight of Multimer: 232.0 kD (experimental) [Gilbert79]

pI: 6.24

Unification Links: ASAP:ABE-0008257 , CGSC:656 , DIP:DIP-36207N , EchoBASE:EB0416 , EcoGene:EG10421 , EcoliWiki:b2508 , Mint:MINT-1235980 , ModBase:P0ADG7 , OU-Microarray:b2508 , PortEco:guaB , PR:PRO_000022851 , Pride:P0ADG7 , Protein Model Portal:P0ADG7 , RefSeq:NP_417003 , RegulonDB:EG10421 , SMR:P0ADG7 , String:511145.b2508 , Swiss-Model:P0ADG7 , UniProt:P0ADG7

Relationship Links: InterPro:IN-FAMILY:IPR000644 , InterPro:IN-FAMILY:IPR001093 , InterPro:IN-FAMILY:IPR005990 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR015875 , Panther:IN-FAMILY:PTHR11911:SF6 , Pfam:IN-FAMILY:PF00478 , Pfam:IN-FAMILY:PF00571 , Prosite:IN-FAMILY:PS00487 , Prosite:IN-FAMILY:PS51371 , Smart:IN-FAMILY:SM00116

In Paralogous Gene Group: 34 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for guaB

GO Terms:

Biological Process: GO:0006164 - purine nucleotide biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0006177 - GMP biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0003938 - IMP dehydrogenase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Gilbert79]
GO:0042802 - identical protein binding Inferred from experiment [Gilbert79]
GO:0000166 - nucleotide binding Inferred by computational analysis [GOA06]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05, Lasserre06]

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides purine biosynthesis
metabolism central intermediary metabolism nucleotide and nucleoside conversions

Essentiality data for guaB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol No 37 Aerobic 7.2 0.35 No [Joyce06]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 4]

Last-Curated ? 04-Jan-2012 by Fulcher C , SRI International

Enzymatic reaction of: IMP dehydrogenase

Synonyms: inosine-5'-monophosphate dehydrogenase, IMPDH, IMP:NAD+ oxidoreductase

EC Number:

IMP + NAD+ + H2O <=> XMP + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the direction shown.

In Pathways: superpathway of histidine, purine, and pyrimidine biosynthesis , superpathway of purine nucleotides de novo biosynthesis II , superpathway of guanosine nucleotides de novo biosynthesis II , guanosine ribonucleotides de novo biosynthesis

IMP dehydrogenase is activated by certain monovalent cations. K+ is the most effective activator, followed by Rb+ and NH4+. Cs+ is the least effective activator. This K+ activation is competitively inhibited by Li+, Na+, Ca2+ and Mg2+. Li+ is a noncompetitive inhibitor with respect to IMP and a competitive inhibitor with respect to NAD. [Kerr00a]

The [Streeter76] citation refers to statements made in that paper regarding the enzyme purified from E. coli B.

Activators (Unknown Mechanism): K+ [Kerr00a, Comment 5] , Rb+ [Kerr00a, Comment 6] , ammonium [Kerr00a, Comment 6] , Cs+ [Kerr00a, Comment 6]

Inhibitors (Competitive): GMP [Gilbert79, Comment 7]

Inhibitors (Unknown Mechanism): 3-deaza-GMP [Streeter76, Helmward89] , ribavirin-5'-monophosphate [Streeter76, Helmward89]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
13.0, 13.2
[Krishnaiah75, BRENDA14]
[Pimkin09a, BRENDA14]
[Krishnaiah75, BRENDA14]
[Pimkin09a, BRENDA14]

Sequence Features

Protein sequence of GuaB with features indicated

Feature Class Location Citations Comment
Mutagenesis-Variant 13
[Kerr97, UniProt12a]
UniProt: Causes a 38-fold increase in the value of Km for K(+). No change is observed in the value of Km for IMP.
Mutagenesis-Variant 50
[Kerr97, UniProt12a]
UniProt: Causes a 17-fold increase in the value of Km for K(+).
Mutagenesis-Variant 54
[Kerr97, UniProt12a]
UniProt: No effect.
Conserved-Region 93 -> 149
UniProt: CBS 1;
Mutagenesis-Variant 138
[Kerr97, UniProt12a]
UniProt: No effect.
Conserved-Region 153 -> 214
UniProt: CBS 2;
Mutagenesis-Variant 200
[Kerr97, UniProt12a]
UniProt: No effect.
Acetylation-Modification 203
Sequence-Conflict 206
[Tiedeman85, UniProt10]
UniProt: (in Ref. 1; CAA26133/AAB18618);
Mutagenesis-Variant 243
[Kerr97, UniProt12a]
UniProt: No effect.
Mutagenesis-Variant 248
[Kerr97, UniProt12a]
UniProt: Causes a 130-fold decrease in the value of kcat.
Amino-Acid-Sites-That-Bind 248
UniProt: NAD; Non-Experimental Qualifier: by similarity.
Nucleotide-Phosphate-Binding-Region 248 -> 250
UniProt: NAD; Non-Experimental Qualifier: by similarity.
N6-acetyllysine-Modification 267
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Nucleotide-Phosphate-Binding-Region 298 -> 300
UniProt: NAD; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 300
UniProt: Potassium; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 302
UniProt: Potassium; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 303
UniProt: IMP; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 305
UniProt: Potassium; via carbonyl oxygen; Non-Experimental Qualifier: by similarity.
Active-Site 305
UniProt: Thioimidate intermediate; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 338
[Kerr97, UniProt12a]
UniProt: Decreases the value of kcat by 600- fold. Increases the value of Km for IMP by 12-fold.
Protein-Segment 338 -> 340
UniProt: IMP binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Protein-Segment 361 -> 362
UniProt: IMP binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Mutagenesis-Variant 369
[Kerr97, UniProt12a]
UniProt: No effect.
Mutagenesis-Variant 373
[Kerr97, UniProt12a]
UniProt: No effect.
Protein-Segment 385 -> 389
UniProt: IMP binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 415
UniProt: IMP; Non-Experimental Qualifier: by similarity.
N6-acetyllysine-Modification 428
[Zhang09, UniProt15]
UniProt: N6-acetyllysine.
Mutagenesis-Variant 469
[Kerr97, UniProt12a]
UniProt: Increases the value of Km for K(+) by 17-fold.
Metal-Binding-Site 469
UniProt: Potassium; via carbonyl oxygen; shared with tetrameric partner; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 470
UniProt: Potassium; via carbonyl oxygen; shared with tetrameric partner; Non-Experimental Qualifier: by similarity.
Metal-Binding-Site 471
UniProt: Potassium; via carbonyl oxygen; shared with tetrameric partner; Non-Experimental Qualifier: by similarity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b2508 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10421; confirmed by SwissProt match.


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."

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Gilbert79: Gilbert HJ, Lowe CR, Drabble WT (1979). "Inosine 5'-monophosphate dehydrogenase of Escherichia coli. Purification by affinity chromatography, subunit structure and inhibition by guanosine 5'-monophosphate." Biochem J 1979;183(3);481-94. PMID: 44191

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."

Hedstrom09: Hedstrom L (2009). "IMP dehydrogenase: structure, mechanism, and inhibition." Chem Rev 109(7);2903-28. PMID: 19480389

Helmward89: Helmward Z "Handbook of Enzyme Inhibitors. 2nd, revised and enlarged edition." Weinheim, Federal Republic of Germany ; New York, NY, USA , 1989.

Hutchings00: Hutchings MI, Drabble WT (2000). "Regulation of the divergent guaBA and xseA promoters of Escherichia coli by the cyclic AMP receptor protein." FEMS Microbiol Lett 187(2);115-22. PMID: 10856643

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Kerr00: Kerr KM, Digits JA, Kuperwasser N, Hedstrom L (2000). "Asp338 controls hydride transfer in Escherichia coli IMP dehydrogenase." Biochemistry 39(32);9804-10. PMID: 10933797

Kerr00a: Kerr KM, Cahoon M, Bosco DA, Hedstrom L (2000). "Monovalent cation activation in Escherichia coli inosine 5'-monophosphate dehydrogenase." Arch Biochem Biophys 2000;375(1);131-7. PMID: 10683258

Kerr97: Kerr KM, Hedstrom L (1997). "The roles of conserved carboxylate residues in IMP dehydrogenase and identification of a transition state analog." Biochemistry 36(43);13365-73. PMID: 9341229

Kozhevnikova12: Kozhevnikova EN, van der Knaap JA, Pindyurin AV, Ozgur Z, van Ijcken WF, Moshkin YM, Verrijzer CP (2012). "Metabolic enzyme IMPDH is also a transcription factor regulated by cellular state." Mol Cell 47(1);133-9. PMID: 22658723

Krishnaiah75: Krishnaiah KV (1975). "Inosinic acid 5'-monophosphate dehydrogenase of Escherichia coli: purification by affinity chromatography and some properties." Arch Biochem Biophys 170(2);567-75. PMID: 1103737

Lambden73: Lambden PR, Drabble WT (1973). "The gua operon of Escherichia coli K-12: evidence for polarity from guaB to guaA." J Bacteriol 115(3);992-1002. PMID: 4353875

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

McLean04: McLean JE, Hamaguchi N, Belenky P, Mortimer SE, Stanton M, Hedstrom L (2004). "Inosine 5'-monophosphate dehydrogenase binds nucleic acids in vitro and in vivo." Biochem J 379(Pt 2);243-51. PMID: 14766016

Nimmesgern99: Nimmesgern E, Black J, Futer O, Fulghum JR, Chambers SP, Brummel CL, Raybuck SA, Sintchak MD (1999). "Biochemical analysis of the modular enzyme inosine 5'-monophosphate dehydrogenase." Protein Expr Purif 17(2);282-9. PMID: 10545277

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Pimkin08: Pimkin M, Markham GD (2008). "The CBS subdomain of inosine 5'-monophosphate dehydrogenase regulates purine nucleotide turnover." Mol Microbiol 68(2);342-59. PMID: 18312263

Pimkin09: Pimkin M, Pimkina J, Markham GD (2009). "A regulatory role of the Bateman domain of IMP dehydrogenase in adenylate nucleotide biosynthesis." J Biol Chem 284(12);7960-9. PMID: 19153081

Pimkin09a: Pimkin M, Markham GD (2009). "Inosine 5'-monophosphate dehydrogenase." Adv Enzymol Relat Areas Mol Biol 76;1-53. PMID: 18990827

Shimada76: Shimada K, Fukumaki Y, Takagi Y (1976). "Expression of the guanine operon of Escherichia coli as analyzed by bacteriophage lambda induced mutations." Mol Gen Genet 147(2);203-8. PMID: 787758

Streeter76: Streeter DG, Koyama HH (1976). "Inhibition of purine nucleotide biosynthesis by 3-deazaguanine, its nucleoside and 5'-nucleotide." Biochem Pharmacol 1976;25(21);2413-5. PMID: 1033766

TesfaSelase92: Tesfa-Selase F, Drabble WT (1992). "Regulation of the gua operon of Escherichia coli by the DnaA protein." Mol Gen Genet 1992;231(2);256-64. PMID: 1736096

Tiedeman85: Tiedeman AA, Smith JM (1985). "Nucleotide sequence of the guaB locus encoding IMP dehydrogenase of Escherichia coli K12." Nucleic Acids Res 1985;13(4);1303-16. PMID: 2860637

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt12: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 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."

Vales79: Vales LD, Chase JW, Murphy JB (1979). "Orientation of the guanine operon of Escherichia coli K-12 by utilizing strains containing guaB-xse and guaB-upp deletions." J Bacteriol 139(1);320-2. PMID: 222730

Yu08: Yu BJ, Kim JA, Moon JH, Ryu SE, Pan JG (2008). "The diversity of lysine-acetylated proteins in Escherichia coli." J Microbiol Biotechnol 18(9);1529-36. PMID: 18852508

Zhang09: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842

Other References Related to Gene Regulation

Andrews88: Andrews SC, Guest JR (1988). "Nucleotide sequence of the gene encoding the GMP reductase of Escherichia coli K12." Biochem J 1988;255(1);35-43. PMID: 2904262

Cho11: Cho BK, Federowicz SA, Embree M, Park YS, Kim D, Palsson BO (2011). "The PurR regulon in Escherichia coli K-12 MG1655." Nucleic Acids Res 39(15);6456-64. PMID: 21572102

Davies96: Davies IJ, Drabble WT (1996). "Stringent and growth-rate-dependent control of the gua operon of Escherichia coli K-12." Microbiology 1996;142 ( Pt 9);2429-37. PMID: 8828209

Fukumaki77: Fukumaki Y, Shimada K, Takagi Y (1977). "Secondary promoter of the guanine operon of Escherichia coli K-12." J Bacteriol 131(2);685-8. PMID: 328493

Husnain08: Husnain SI, Thomas MS (2008). "Downregulation of the Escherichia coli guaB promoter by FIS." Microbiology 154(Pt 6);1729-38. PMID: 18524927

Husnain08a: Husnain SI, Thomas MS (2008). "The UP element is necessary but not sufficient for growth rate-dependent control of the Escherichia coli guaB promoter." J Bacteriol 190(7);2450-7. PMID: 18203835

Husnain09: Husnain SI, Busby SJ, Thomas MS (2009). "Downregulation of the Escherichia coli guaB promoter by upstream-bound cyclic AMP receptor protein." J Bacteriol 191(19);6094-104. PMID: 19633076

Kim13: Kim HJ, Hou BK, Lee SG, Kim JS, Lee DW, Lee SJ (2013). "Genome-wide analysis of redox reactions reveals metabolic engineering targets for D-lactate overproduction in Escherichia coli." Metab Eng 18;44-52. PMID: 23563322

Meng90: Meng LM, Kilstrup M, Nygaard P (1990). "Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli." Eur J Biochem 1990;187(2);373-9. PMID: 2404765

TesfaSelase96: Tesfa-Selase F, Drabble WT (1996). "Specific binding of DnaA protein to a DnaA box in the guaB gene of Escherichia coli K12." Eur J Biochem 241(2);411-6. PMID: 8917437

Tiedeman85a: Tiedeman AA, Smith JM, Zalkin H (1985). "Nucleotide sequence of the guaA gene encoding GMP synthetase of Escherichia coli K12." J Biol Chem 1985;260(15);8676-9. PMID: 3894345

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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