Escherichia coli K-12 substr. MG1655 Enzyme: formyltetrahydrofolate deformylase

Gene: purU Accession Numbers: EG11819 (EcoCyc), b1232, ECK1227

Synonyms: ychI, tgs, formyl-FH(4) hydrolase

Regulation Summary Diagram: ?

Regulation summary diagram for purU

Subunit composition of formyltetrahydrofolate deformylase = [PurU]6
         formyltetrahydrofolate deformylase = PurU

FormylTHF deformylase appears to have two roles in E. coli metabolism. The first role is to provide the major source of formate to the cell under aerobic growth conditions. This was supported by the fact that a purU purN double mutant shows auxotrophy for either purine or formate under aerobic conditions. The second and possibly major role is to balance the pools of THF and 1-C-THF to ensure that synthesis of glycine can be maintained when the cell has excess purines, methionine and histidine and the biosynthetic pathways for these molecules are shut down [Nagy93, Nagy95].

A hybrid protein created by assembling the C-terminal (N10-formyltetrahydrofolate binding) region of PurU and the N-terminal region of the purN gene (GAR binding region) shows better activity and stability in terms of glycinamide ribonucleotide (GAR) transformylase activity [Nixon97].

This enzyme contains an ACT domain at the N-terminus. This is an amino acid binding domain that functions in allosteric regulation [Collakova08].

Locations: cytosol

Map Position: [1,287,005 <- 1,287,847] (27.74 centisomes, 100°)
Length: 843 bp / 280 aa

Molecular Weight of Polypeptide: 31.935 kD (from nucleotide sequence), 32 kD (experimental) [Bosl94 ]

Unification Links: ASAP:ABE-0004138 , CGSC:35231 , EchoBASE:EB1766 , EcoGene:EG11819 , EcoliWiki:b1232 , Entrez-gene:945827 , ModBase:P37051 , OU-Microarray:b1232 , PortEco:purU , PR:PRO_000023646 , Pride:P37051 , Protein Model Portal:P37051 , RefSeq:NP_415748 , RegulonDB:EG11819 , SMR:P37051 , String:511145.b1232 , UniProt:P37051

Relationship Links: InterPro:IN-FAMILY:IPR002376 , InterPro:IN-FAMILY:IPR002912 , InterPro:IN-FAMILY:IPR004810 , Panther:IN-FAMILY:PTHR10520:SF7 , Pfam:IN-FAMILY:PF00551 , Pfam:IN-FAMILY:PF01842 , Prints:IN-FAMILY:PR01575 , Prosite:IN-FAMILY:PS51671

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006164 - purine nucleotide biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA11, Nagy93]
GO:0009152 - purine ribonucleotide biosynthetic process Inferred from experiment [Nagy95]
GO:0006189 - 'de novo' IMP biosynthetic process Inferred by computational analysis [UniProtGOA12, GOA06, GOA01]
GO:0006730 - one-carbon metabolic process Author statement Inferred by computational analysis [UniProtGOA11, deCrecyLagard07]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
GO:0009058 - biosynthetic process Inferred by computational analysis [GOA01]
GO:0009257 - 10-formyltetrahydrofolate biosynthetic process Author statement [deCrecyLagard07]
Molecular Function: GO:0008864 - formyltetrahydrofolate deformylase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, GOA01, Nagy95]
GO:0016597 - amino acid binding Inferred by computational analysis [GOA01]
GO:0016742 - hydroxymethyl-, formyl- and related transferase activity Inferred by computational analysis [GOA01]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm

MultiFun Terms: metabolism biosynthesis of building blocks nucleotides purine ribonucleotide biosynthesis
metabolism central intermediary metabolism formyl-THF biosynthesis

Essentiality data for purU knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Reviewed 26-Feb-2010 by Sarker M

Enzymatic reaction of: formyltetrahydrofolate deformylase

Synonyms: formyltetrahydrofolate hydrolase, 10-formyltetrahydrofolate amidohydrolase

EC Number:

an N10-formyl-tetrahydrofolate + H2O <=> a tetrahydrofolate + formate + 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.

The reaction is irreversible in the direction shown. [Nagy95]

Alternative Substrates [Comment 4]:

Activators (Unknown Mechanism): L-methionine [Nagy95]

Inhibitors (Unknown Mechanism): glycine [Nagy95]

Kinetic Parameters:

Km (μM)
an N10-formyl-tetrahydrofolate

Sequence Features

Protein sequence of formyltetrahydrofolate deformylase with features indicated

Feature Class Location Citations Comment
Conserved-Region 8 -> 86
UniProt: ACT.
Active-Site 225
UniProt: Non-Experimental Qualifier: by similarity;
Acetylation-Modification 264

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b1232 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11819; 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

Bosl94: Bosl M, Kersten H (1994). "Organization and functions of genes in the upstream region of tyrT of Escherichia coli: phenotypes of mutants with partial deletion of a new gene (tgs)." J Bacteriol 176(1);221-31. PMID: 8282700

Collakova08: Collakova E, Goyer A, Naponelli V, Krassovskaya I, Gregory JF, Hanson AD, Shachar-Hill Y (2008). "Arabidopsis 10-formyl tetrahydrofolate deformylases are essential for photorespiration." Plant Cell 20(7);1818-32. PMID: 18628352

deCrecyLagard07: de Crecy-Lagard V, El Yacoubi B, de la Garza RD, Noiriel A, Hanson AD (2007). "Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations." BMC Genomics 8;245. PMID: 17645794

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

Nagy93: Nagy PL, McCorkle GM, Zalkin H (1993). "purU, a source of formate for purT-dependent phosphoribosyl-N-formylglycinamide synthesis." J Bacteriol 175(21);7066-73. PMID: 8226647

Nagy95: Nagy PL, Marolewski A, Benkovic SJ, Zalkin H (1995). "Formyltetrahydrofolate hydrolase, a regulatory enzyme that functions to balance pools of tetrahydrofolate and one-carbon tetrahydrofolate adducts in Escherichia coli." J Bacteriol 1995;177(5);1292-8. PMID: 7868604

Nixon97: Nixon AE, Warren MS, Benkovic SJ (1997). "Assembly of an active enzyme by the linkage of two protein modules." Proc Natl Acad Sci U S A 94(4);1069-73. PMID: 9037007

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

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 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."

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

Other References Related to Gene Regulation

Herrington13: Herrington MB, Sitaras C (2013). "The influence of CsgD on the expression of genes of folate metabolism and hmp in Escherichia coli K-12." Arch Microbiol 195(8);559-69. PMID: 23824318

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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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