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Escherichia coli K-12 substr. MG1655 Enzyme: S-formylglutathione hydrolase



Gene: frmB Accession Numbers: G6208 (EcoCyc), b0355, ECK0352

Synonyms: yaiM

Regulation Summary Diagram: ?

Summary:
FrmB is a promiscuous serine hydrolase; its highest specific activity is with the substrate S-formylglutathione. Sulfhydryl inhibitors affect enzymatic activity [Gonzalez06].

FrmB is encoded in an operon with FrmR and FrmA, which are proteins involved in the oxidation of formaldehyde. FrmB has similarity to the S-formylglutathione hydrolase of Paracoccus denitrificans [Herring04] and a paralog, YeiG [Gonzalez06].

Formaldehyde stimulates expression of frmB 45-fold in wild type and 70-fold in a yeiG deletion background. Under normal growth conditions, neither a frmB deletion mutant nor a frmB yeiG double mutant have a detectable growth defect. Addition of 0.4 mM formaldehyde to the growth medium caused only a small growth defect in the frmB single mutant, while the growth rate of the double mutant drops to 43% of wild type [Gonzalez06].

Locations: cytosol

Map Position: [376,759 <- 377,592] (8.12 centisomes)
Length: 834 bp / 277 aa

Molecular Weight of Polypeptide: 31.424 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0001219 , DIP:DIP-11274N , EchoBASE:EB3080 , EcoGene:EG13295 , EcoliWiki:b0355 , ModBase:P51025 , OU-Microarray:b0355 , PortEco:frmB , PR:PRO_000022695 , Protein Model Portal:P51025 , RefSeq:NP_414889 , RegulonDB:G6208 , SMR:P51025 , String:511145.b0355 , Swiss-Model:P51025 , UniProt:P51025

Relationship Links: InterPro:IN-FAMILY:IPR000801 , InterPro:IN-FAMILY:IPR014186 , Panther:IN-FAMILY:PTHR10061 , Pfam:IN-FAMILY:PF00756

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0046292 - formaldehyde metabolic process Inferred from experiment [Gonzalez06]
GO:0046294 - formaldehyde catabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0018738 - S-formylglutathione hydrolase activity Inferred from experiment Inferred by computational analysis [GOA01, GOA01a, Gonzalez06]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11a]
GO:0052689 - carboxylic ester hydrolase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell processes protection detoxification

Essentiality data for frmB 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]

Credits:
Last-Curated ? 29-Mar-2006 by Keseler I , SRI International


Enzymatic reaction of: S-formylglutathione hydrolase

EC Number: 3.1.2.12

S-formylglutathione + H2O <=> formate + glutathione + 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 physiologically favored in the direction shown.

Alternative Substrates for S-formylglutathione: p-nitrophenyl propionate [Gonzalez06 ] , (R)-S-lactoylglutathione [Gonzalez06 ]

In Pathways: formaldehyde oxidation II (glutathione-dependent)

Summary:
The enzyme shows a sigmoidal saturation curve, indicating positive cooperativity in S-formylglutathione binding. High concentrations of S-formylglutathione inhibit the enzymatic activity [Gonzalez06].

Inhibitors (Unknown Mechanism): Cu2+ [Gonzalez06] , Zn2+ [Gonzalez06] , N-ethylmaleimide [Gonzalez06] , iodoacetate [Gonzalez06]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
S-formylglutathione
430.0, 410.0
6.51, 28.5
[Gonzalez06, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Active-Site 145
[UniProt10a]
UniProt: Charge relay system; Non-Experimental Qualifier: by similarity;
Active-Site 221
[UniProt10a]
UniProt: Charge relay system; Non-Experimental Qualifier: by similarity;
Active-Site 254
[UniProt10a]
UniProt: Charge relay system; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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." http://www.brenda-enzymes.org.

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

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."

Gonzalez06: Gonzalez CF, Proudfoot M, Brown G, Korniyenko Y, Mori H, Savchenko AV, Yakunin AF (2006). "Molecular basis of formaldehyde detoxification: Characterization of two s-formylglutathione hydrolases from Escherichia coli, FrmB and YeiG." J Biol Chem 281:14514-14522. PMID: 16567800

Herring04: Herring CD, Blattner FR (2004). "Global transcriptional effects of a suppressor tRNA and the inactivation of the regulator frmR." J Bacteriol 186(20);6714-20. PMID: 15466022

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

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

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


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 18.5 on Sat Dec 20, 2014, biocyc13.