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Escherichia coli K-12 substr. MG1655 Enzyme: 2,4-dienoyl-CoA reductase



Gene: fadH Accession Numbers: G36 (EcoCyc), b3081, ECK3071

Synonyms: ygjL

Regulation Summary Diagram: ?

Summary:
2,4-Dienoyl-CoA reductase functions in the reductive removal of double bonds extending from even-numbered carbon atoms in unsaturated and polyunsaturated fatty acids.

The product of the reaction catalyzed by E. coli FadH is 2-trans-enoyl-CoA, in contrast with the bovine enzyme, which produces 3-trans-enoyl-CoA. FadH is able to catalyze the reduction of 2-trans,4-cis and 2-trans,4-trans isomers with almost equal efficiency [Dommes84]. This is not due to a cis-trans isomerase activity of the enzyme [Liang00]. Kinetic data first suggested that the reaction proceeds via a ping-pong mechanism [He97]. A crystal structure of the enzyme has been solved at 2.2 Å resolution. A possible electron transfer pathway from the electron source, NADPH, via FAD, the 4Fe-4S cluster, and FMN was proposed, and the authors conclude that a ping-pong kinetic mechanism is unlikely [Hubbard03]. Site-directed mutagenesis was used to identify residues involved in catalysis and to support the proposed reaction mechanism [Tu08].

Expression is induced by growth on oleate and is subject to catabolite repression [Dommes84, You89]. Regulation of fadH expression was later shown to be complex and involves three independent regulators, FadR, ArcA, and cAMP-CRP [Feng10, Feng12] as well as HipB [Lin13].

Citations: [Mizugaki82, Mizugaki82a, Mizugaki83, Kimura04]

Locations: cytosol

Map Position: [3,229,687 -> 3,231,705] (69.61 centisomes)
Length: 2019 bp / 672 aa

Molecular Weight of Polypeptide: 72.678 kD (from nucleotide sequence), 73.0 kD (experimental) [Dommes84 ]

pI: 6.55 [He97]

Unification Links: ASAP:ABE-0010124 , DIP:DIP-9562N , EchoBASE:EB2582 , EcoGene:EG12723 , EcoliWiki:b3081 , ModBase:P42593 , OU-Microarray:b3081 , PortEco:fadH , PR:PRO_000022570 , Pride:P42593 , Protein Model Portal:P42593 , RefSeq:NP_417552 , RegulonDB:G36 , SMR:P42593 , String:511145.b3081 , UniProt:P42593

Relationship Links: InterPro:IN-FAMILY:IPR001155 , InterPro:IN-FAMILY:IPR013027 , InterPro:IN-FAMILY:IPR013785 , InterPro:IN-FAMILY:IPR023753 , PDB:Structure:1PS9 , Pfam:IN-FAMILY:PF00724 , Pfam:IN-FAMILY:PF07992 , Prints:IN-FAMILY:PR00368

In Paralogous Gene Group: 324 (2 members) , 487 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0033543 - fatty acid beta-oxidation, unsaturated, even number, reductase/isomerase pathway Inferred from experiment [You89]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008670 - 2,4-dienoyl-CoA reductase (NADPH) activity Inferred from experiment Inferred by computational analysis [GOA01, You89, Dommes84]
GO:0010181 - FMN binding Inferred from experiment Inferred by computational analysis [GOA01a, Liang00]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Liang00]
GO:0071949 - FAD binding Inferred from experiment [Dommes84]
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]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks fatty acids and phosphatidic acid
metabolism carbon utilization fatty acids

Essentiality data for fadH 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]

Credits:
Last-Curated ? 08-Jul-2014 by Keseler I , SRI International


Enzymatic reaction of: 2,4-dienoyl-CoA reductase

Synonyms: 2,4-dienoyl-CoA reductase (NADPH), 4-enoyl-CoA reductase (NADPH), trans-2,3-didehydroacyl-CoA:NADP+ 4-oxidoreductase, DCR

EC Number: 1.3.1.34

trans-Δ2, cis-Δ4-decadienoyl-CoA + NADPH + H+ <=> trans-Δ2-decenoyl-CoA + NADP+

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 physiologically favored in the direction shown.

Alternative Substrates for trans-Δ2, cis-Δ4-decadienoyl-CoA [Comment 4 ]: trans,trans-2,4-decadienoyl-CoA [Dommes84 , Dommes82 ]

Summary:
The enzyme is inhibited by both substrate and NADPH at higher concentrations [Dommes84].

Cofactors or Prosthetic Groups: a [4Fe-4S] iron-sulfur cluster [Comment 5, Liang00], FMN [Comment 6, Liang00], FAD [Comment 7, Dommes84]

Inhibitors (Competitive): trans-Δ2, cis-Δ4-decadienoyl-CoA [Dommes84]

Inhibitors (Noncompetitive): NADH [Dommes84]

Inhibitors (Unknown Mechanism): p-chloromercuribenzoate [Dommes84]

Primary Physiological Regulators of Enzyme Activity: NADH

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
trans,trans-2,4-decadienoyl-CoA
2.3
16.0
[He97]
NADPH
50.0
[He97, BRENDA14]
NADPH
0.8
9.5
[Tu08, BRENDA14]

pH(opt): 7.4 [BRENDA14, Mizugaki82]


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[He97, UniProt11]
UniProt: Removed.
Chain 2 -> 672
[UniProt09]
UniProt: 2,4-dienoyl-CoA reductase [NADPH];
Metal-Binding-Site 335
[UniProt10b]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 338
[UniProt10b]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 342
[UniProt10b]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 354
[UniProt10b]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Acetylation-Modification 564
[Yu08]
 


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
4/2/1999 (pkarp) Merged genes G7600/b3081 and G36/fadH
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

Dommes82: Dommes V, Luster W, Cvetanovic M, Kunau WH (1982). "Purification by affinity chromatography of 2,4-dienoyl-CoA reductases from bovine liver and Escherichia coli." Eur J Biochem 125(2);335-41. PMID: 6749495

Dommes84: Dommes V, Kunau WH (1984). "2,4-Dienoyl coenzyme A reductases from bovine liver and Escherichia coli. Comparison of properties." J Biol Chem 1984;259(3);1781-8. PMID: 6363415

Feng10: Feng Y, Cronan JE (2010). "Overlapping Repressor Binding Sites Result in Additive Regulation of Escherichia coli FadH by FadR and ArcA." J Bacteriol 192(17);4289-99. PMID: 20622065

Feng12: Feng Y, Cronan JE (2012). "Crosstalk of Escherichia coli FadR with global regulators in expression of fatty acid transport genes." PLoS One 7(9);e46275. PMID: 23029459

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."

He97: He XY, Yang SY, Schulz H (1997). "Cloning and expression of the fadH gene and characterization of the gene product 2,4-dienoyl coenzyme A reductase from Escherichia coli." Eur J Biochem 1997;248(2);516-20. PMID: 9346310

Hubbard03: Hubbard PA, Liang X, Schulz H, Kim JJ (2003). "The crystal structure and reaction mechanism of Escherichia coli 2,4-dienoyl-CoA reductase." J Biol Chem 278(39);37553-60. PMID: 12840019

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

Kimura04: Kimura C, Mizugaki M, Yamanaka H, Fujino M, Morishima T (2004). "[2,4-Dienoyl-CoA reductases: from discovery toward pathophysiological significance]." Nihon Rinsho 62(8);1577-83. PMID: 15344554

Liang00: Liang X, Thorpe C, Schulz H (2000). "2,4-Dienoyl-CoA reductase from Escherichia coli is a novel iron-sulfur flavoprotein that functions in fatty acid beta-oxidation." Arch Biochem Biophys 2000;380(2);373-9. PMID: 10933894

Lin13: Lin CY, Awano N, Masuda H, Park JH, Inouye M (2013). "Transcriptional Repressor HipB Regulates the Multiple Promoters in Escherichia coli." J Mol Microbiol Biotechnol 23(6);440-447. PMID: 24089053

Mizugaki82: Mizugaki M, Nishimaki T, Yamamoto H, Nishimura S, Sagi M, Yamanaka H (1982). "Studies on the metabolism of unsaturated fatty acids. VIII. Induction of 2,4-dienoyl-CoA reductase in Escherichia coli on the addition of unsaturated fatty acids." J Biochem 91(4);1453-6. PMID: 7047514

Mizugaki82a: Mizugaki M, Kimura C, Nishimaki T, Yamamoto H, Sagi M, Nishimura S, Yamanaka H (1982). "Studies on the metabolism of unsaturated fatty acids. X. Purification and some properties of 2,4-dienoyl-CoA reductase from Escherichia coli." J Biochem 92(5);1671-4. PMID: 6759505

Mizugaki83: Mizugaki M, Kimura C, Nishimaki T, Kawaguchi A, Okuda S, Yamanaka H (1983). "Studies on the metabolism of unsaturated fatty acids. XII. Reaction catalyzed by 2,4-dienoyl-CoA reductase of Escherichia coli." J Biochem 94(2);409-13. PMID: 6355075

Tu08: Tu X, Hubbard PA, Kim JJ, Schulz H (2008). "Two distinct proton donors at the active site of Escherichia coli 2,4-dienoyl-CoA reductase are responsible for the formation of different products." Biochemistry 47(4);1167-75. PMID: 18171025

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

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

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

You89: You SY, Cosloy S, Schulz H (1989). "Evidence for the essential function of 2,4-dienoyl-coenzyme A reductase in the beta-oxidation of unsaturated fatty acids in vivo. Isolation and characterization of an Escherichia coli mutant with a defective 2,4-dienoyl-coenzyme A reductase." J Biol Chem 1989;264(28);16489-95. PMID: 2506179

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

Cho06: Cho BK, Knight EM, Palsson BO (2006). "Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA." Microbiology 152(Pt 8);2207-19. PMID: 16849788


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 Mon Dec 22, 2014, BIOCYC13A.