Escherichia coli K-12 substr. MG1655 Enzyme: isochorismate synthase 2

Gene: menF Accession Numbers: EG12362 (EcoCyc), b2265, ECK2259

Synonyms: yfbA

Regulation Summary Diagram: ?

Regulation summary diagram for menF

Subunit composition of isochorismate synthase 2 = [MenF]2

There are two isochorismate synthase enzymes present in E. coli, encoded by menF and entC. MenF is specific to the menaquinone biosynthetic pathway, while EntC is specific to the enterobactin biosynthetic pathway [Dahm98]. Isochorismate synthase activity due to MenF is increased under anaerobiosis, while activity due to EntC is increased by iron limitation [Buss01]. Reports differ on whether [Dahm98] or not [Daruwala97] the reaction catalyzed by MenF is reversible.

Crystal structures of MenF have been solved at 2.5 Å and 2 Å resolution [Kolappan07, Parsons08]. The Lys190 residue has been identified as the catalytic base, and a reaction mechanism involving the nucleophilic attack of a water molecule on the isochorismate ring has been proposed [Kolappan07]. The active site appears to contain both the required Mg2+ cofactor and a pair of sulfates [Parsons08].

An entC single mutant is defective in enterobactin, but not menaquinone biosynthesis [Muller96, Kwon96a], while an entC menF double mutant is defective in both enterobactin and menaquinone biosynthesis [Muller96]. A menF mutant produces only trace amounts of menaquinone unless supplemented with o-succinylbenzoate [Dahm98]. Expression of menF from a plasmid rescues the enterobactin biosynthesis defect of an entC mutant [Muller96].

Review: [Dosselaere01]

Gene Citations: [Sharma96]

Locations: cytosol

Map Position: [2,377,370 <- 2,378,665] (51.24 centisomes, 184°)
Length: 1296 bp / 431 aa

Molecular Weight of Polypeptide: 48.765 kD (from nucleotide sequence), 49 kD (experimental) [Daruwala96 ]

Molecular Weight of Multimer: 98 kD (experimental) [Daruwala97]

Isozyme Sequence Similarity:
isochorismate synthase 1: YES

Unification Links: ASAP:ABE-0007485 , CGSC:35955 , DIP:DIP-10187N , EchoBASE:EB2265 , EcoGene:EG12362 , EcoliWiki:b2265 , Mint:MINT-1275996 , ModBase:P38051 , OU-Microarray:b2265 , PortEco:menF , PR:PRO_000023205 , Pride:P38051 , Protein Model Portal:P38051 , RefSeq:NP_416768 , RegulonDB:EG12362 , SMR:P38051 , String:511145.b2265 , UniProt:P38051

Relationship Links: InterPro:IN-FAMILY:IPR004561 , InterPro:IN-FAMILY:IPR005801 , InterPro:IN-FAMILY:IPR015890 , Panther:IN-FAMILY:PTHR11236:SF3 , PDB:Structure:2EUA , PDB:Structure:3BZM , PDB:Structure:3BZN , Pfam:IN-FAMILY:PF00425

In Paralogous Gene Group: 161 (4 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0009234 - menaquinone biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, Dahm98]
GO:0009058 - biosynthetic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0000287 - magnesium ion binding Inferred from experiment [Parsons08]
GO:0008909 - isochorismate synthase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Daruwala97]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers menaquinone, ubiquinone
metabolism energy metabolism, carbon anaerobic respiration

Essentiality data for menF 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 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Curated 07-Jul-2008 by Keseler I , SRI International
Last-Curated ? 22-Sep-2008 by Shearer A , SRI International

Enzymatic reaction of: isochorismate synthase

Synonyms: isochorismate hydroxymutase, menaquinone-specific isochorismate synthase, isochorismate synthase, menaquinone-specific

EC Number:

chorismate <=> isochorismate

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

This reaction is reversible.

In Pathways: superpathway of menaquinol-8 biosynthesis I , superpathway of chorismate metabolism , 1,4-dihydroxy-2-naphthoate biosynthesis I

Cofactors or Prosthetic Groups: Mg2+ [Dahm98, Daruwala97]

Regulators of Unknown Type: N-ethylmaleimide [Daruwala97] , 2-mercaptoethanol [Daruwala97] , L-dithiothreitol [Daruwala97]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Kolappan07, BRENDA14]
[Sridharan10, BRENDA14]
[Liu90, BRENDA14]
1.33, 2.93
0.0068, 0.015
[Daruwala97, BRENDA14]
[Liu90, BRENDA14]

T(opt): 37 °C [BRENDA14, Daruwala97]

pH(opt): 6.5 [BRENDA14, Daruwala97], 7.5 [BRENDA14, Daruwala97], 7.5-8 [Daruwala97]

Sequence Features

Protein sequence of MenF with features indicated

Feature Class Location Common Name Citations Comment
Mutagenesis-Variant 190  
[Kolappan07, UniProt14a]
UniProt: Lack of activity.
Active-Site 190 catalytic base
Lys190 is the catalytic base residue.
Mutagenesis-Variant 240  
[Kolappan07, UniProt14a]
UniProt: Lack of activity.
Active-Site 240  
[Kolappan07, UniProt14a]
UniProt: Proton donor.
Mutagenesis-Variant 255  
[Kolappan07, UniProt14a]
UniProt: Decrease in activity.
Metal-Binding-Site 284  
[Parsons08, UniProt14a]
UniProt: Magnesium.
Sequence-Conflict 310 -> 312  
[Daruwala96, UniProt10a]
UniProt: (in Ref. 3; AAC44303);
Mutagenesis-Variant 344  
[Kolappan07, UniProt14a]
UniProt: Lack of activity.
Mutagenesis-Variant 387  
[Kolappan07, UniProt14a]
UniProt: Lack of activity.
Metal-Binding-Site 416  
[Parsons08, UniProt14a]
UniProt: Magnesium.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b2265 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12362; 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."

Buss01: Buss K, Muller R, Dahm C, Gaitatzis N, Skrzypczak-Pietraszek E, Lohmann S, Gassen M, Leistner E (2001). "Clustering of isochorismate synthase genes menF and entC and channeling of isochorismate in Escherichia coli." Biochim Biophys Acta 1522(3);151-7. PMID: 11779629

Dahm98: Dahm C, Muller R, Schulte G, Schmidt K, Leistner E (1998). "The role of isochorismate hydroxymutase genes entC and menF in enterobactin and menaquinone biosynthesis in Escherichia coli." Biochim Biophys Acta 1425(2);377-86. PMID: 9795253

Daruwala96: Daruwala R, Kwon O, Meganathan R, Hudspeth ME (1996). "A new isochorismate synthase specifically involved in menaquinone (vitamin K2) biosynthesis encoded by the menF gene." FEMS Microbiol Lett 1996;140(2-3);159-63. PMID: 8764478

Daruwala97: Daruwala R, Bhattacharyya DK, Kwon O, Meganathan R (1997). "Menaquinone (vitamin K2) biosynthesis: overexpression, purification, and characterization of a new isochorismate synthase from Escherichia coli." J Bacteriol 1997;179(10);3133-8. PMID: 9150206

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

Dosselaere01: Dosselaere F, Vanderleyden J (2001). "A metabolic node in action: chorismate-utilizing enzymes in microorganisms." Crit Rev Microbiol 27(2);75-131. PMID: 11450855

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

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."

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

Kolappan07: Kolappan S, Zwahlen J, Zhou R, Truglio JJ, Tonge PJ, Kisker C (2007). "Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family." Biochemistry 46(4);946-53. PMID: 17240978

Kwon96a: Kwon O, Hudspeth ME, Meganathan R (1996). "Anaerobic biosynthesis of enterobactin Escherichia coli: regulation of entC gene expression and evidence against its involvement in menaquinone (vitamin K2) biosynthesis." J Bacteriol 1996;178(11);3252-9. PMID: 8655506

Liu90: Liu J, Quinn N, Berchtold GA, Walsh CT (1990). "Overexpression, purification, and characterization of isochorismate synthase (EntC), the first enzyme involved in the biosynthesis of enterobactin from chorismate." Biochemistry 1990;29(6);1417-25. PMID: 2139795

Muller96: Muller R, Dahm C, Schulte G, Leistner E (1996). "An isochorismate hydroxymutase isogene in Escherichia coli." FEBS Lett 1996;378(2);131-4. PMID: 8549818

Parsons08: Parsons JF, Shi KM, Ladner JE (2008). "Structure of isochorismate synthase in complex with magnesium." Acta Crystallogr D Biol Crystallogr 64(Pt 5);607-10. PMID: 18453696

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Sharma96: Sharma V, Hudspeth ME, Meganathan R (1996). "Menaquinone (vitamin K2) biosynthesis: localization and characterization of the menE gene from Escherichia coli." Gene 1996;168(1);43-8. PMID: 8626063

Sridharan10: Sridharan S, Howard N, Kerbarh O, Blaszczyk M, Abell C, Blundell TL (2010). "Crystal structure of Escherichia coli enterobactin-specific isochorismate synthase (EntC) bound to its reaction product isochorismate: implications for the enzyme mechanism and differential activity of chorismate-utilizing enzymes." J Mol Biol 397(1);290-300. PMID: 20079748

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt14a: UniProt Consortium (2014). "UniProt version 2014-08 released on 2014-08-01 00:00:00." Database.

UniProtGOA11: 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."

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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 Oct 13, 2015, BIOCYC14A.