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Escherichia coli K-12 substr. MG1655 Enzyme: 3-hydroxydecanoyl-[acp] dehydrase



Gene: fabA Accession Numbers: EG10273 (EcoCyc), b0954, ECK0945

Synonyms: β-hydroxyacyl-ACP dehydratase/isomerase, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA

Regulation Summary Diagram: ?

Subunit composition of 3-hydroxydecanoyl-[acp] dehydrase = [FabA]2

Summary:
FabA is a dehydratase/isomerase that plays a specific and essential role in the synthesis of unsaturated fatty acids. It functions at the branch point between saturated and unsaturated fatty acid biosynthesis by introducing cis unsaturation (see pathway cis-dodecenoyl biosynthesis). It is responsible for shunting an intermediate in the biosynthetic pathway for saturated fatty acids, a trans2-decenoyl-[acp], into unsaturated products (see below). In contrast to FabA, a second dehydratase encoded by fabZ lacks isomerase activity and plays a general role in both saturated and unsaturated fatty acid biosynthesis [Heath96].

The bifunctional FabA catalyzes the dehydration of an (R)-3-hydroxydecanoyl-[acp] to a trans2-decenoyl-[acp] (E-(2)-decenoyl-[acp]) and its isomeriaztion to a cis3-decenoyl-[acp] (Z-(3)-decenoyl-[acp]). During this reaction, enzyme-bound a trans2-decenoyl-[acp] is isomerized to a cis3-decenoyl-[acp] and the cis double bond is preserved during the subsequent rounds of elongation that ultimately produce the unsaturated fatty acids palmitoleate and cis-vaccenate (see pathways palmitoleate biosynthesis I and cis-vaccenate biosynthesis). a trans2-decenoyl-[acp] can also be released from the enzyme and utilized in the synthesis of saturated fatty acids (see pathway palmitate biosynthesis II (bacteria and plants)).

The dehydratase activity of FabA catalyzes the dehydration of saturated β-hydroxyacyl-[acp] substrates and is most active on substrates of intermediate chain length. It prefers substrates with C10 aliphatic chains in vitro and does not use unsaturated substrates [Heath96, Leesong96].

A temperature-sensitive mutant of fabA was isolated that was unable to synthesize unsaturated fatty acids at nonpermissive temperatures and required an exogenous source of unsaturated fatty acids [Cronan73]. Overexpression of FabA was shown to increase saturated fatty acid levels in membrane phospholipids, with no increase in unsaturated fatty acid levels. This indicated that although the activity of FabA is necessary for unsaturated fatty acid synthesis, its activity does not limit the rate of unsaturated fatty acid synthesis under normal growth conditions [Clark83].

In early work from the laboratory of Konrad Bloch, this enzyme (β-hydroxydecanoyl thioester dehydratase) was purified and characterized from E. coli B [NORRIS64, Brock67, Kass67, Helmkamp68, Helmkamp69, Endo70, Morisaki72, Matsuo92]. The reaction mechanism has been studied in detail [Schwab84a, Schwab84b, Schwab84, Schwab86, Annand93]. The enzyme from E. coli K-12 was identified as the product of fabA [Cronan73].

The enzyme was crystallized [Sharma90] and the crystal structures of free FabA, and FabA in complex with the mechanism-activated "suicide" inhibitor 3-decynoyl-N-acetylcysteamine, were determined at 2.0 Å resolution [Leesong96]. The enzyme forms a symmetric dimer with an unusual α+β hot dog fold. Dimerization is essential for activity. Each active site is located at the interface between the two subunits forming a tunnel-shaped pocket that is not accessible to the solvent. Active site histidine and aspartate residues were identified as reactive groups [Leesong96]. 3-decynoyl-N-acetylcysteamine forms a covalent adduct with the active site histidine residue resulting in loss of activity [Cronan88, Leesong96].

A dehydratase/isomerase enzyme that is functionally analogous to that of E. coli FabA was identified in the Gram-positive bacterium Enterococcus faecalis as FabZ1. Although it could functionally replace FabA in E. coli, its amino acid sequence more closely resembled E. coli FabZ [Wang04a]. In metabolic engineering studies, overexpression of fabA and fabB along with a heterologous thioesterase resulted in efficient production of unsaturated fatty acids in E. coli [Cao10]. Active FabA has also been expressed in transgenic tobacco plants [Saito95]. A general dehydratase-specific reactive probe has been designed based upon studies using FabA [Ishikawa12].

The fabA gene is regulated at the transcriptional level by the FadR activator and the FabR repressor, which control unsaturated fatty acid biosynthesis in E. coli. FadR predominately regulates fabA expression, whereas FabR is the dominant regulator of fabB expression [Feng11].

Reviews: [White05, Magnuson93], and Cronan, J.E. and C.O. Rock (2008) "Biosynthesis of Membrane Lipids" EcoSal 3.6.4 [ECOSAL]

Gene Citations: [Cronan72, Nunn83, Henry92, Feng09]

Locations: cytosol

Map Position: [1,015,175 <- 1,015,693] (21.88 centisomes)
Length: 519 bp / 172 aa

Molecular Weight of Polypeptide: 18.969 kD (from nucleotide sequence)

pI: 6.53

Isozyme Sequence Similarity:
FabZ: YES

Unification Links: ASAP:ABE-0003229 , CGSC:799 , DIP:DIP-31864N , EchoBASE:EB0269 , EcoGene:EG10273 , EcoliWiki:b0954 , Mint:MINT-1218658 , OU-Microarray:b0954 , PortEco:fabA , PR:PRO_000022559 , Pride:P0A6Q3 , Protein Model Portal:P0A6Q3 , RefSeq:NP_415474 , RegulonDB:EG10273 , SMR:P0A6Q3 , String:511145.b0954 , UniProt:P0A6Q3

Relationship Links: InterPro:IN-FAMILY:IPR010083 , InterPro:IN-FAMILY:IPR013114 , PDB:Structure:1MKA , PDB:Structure:1MKB , Pfam:IN-FAMILY:PF07977

In Paralogous Gene Group: 60 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0006633 - fatty acid biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01, Feng09, Cronan73]
GO:0008610 - lipid biosynthetic process Inferred from experiment [Feng09]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0006631 - fatty acid metabolic process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0008693 - 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Heath96]
GO:0034017 - trans-2-decenoyl-acyl-carrier-protein isomerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Guerra90]
GO:0042803 - protein homodimerization activity Inferred from experiment [Helmkamp69]
GO:0047451 - 3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity Inferred from experiment Inferred by computational analysis [GOA01a, Heath96]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01]

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

Essentiality data for fabA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 1]

Credits:
Last-Curated ? 15-May-2013 by Fulcher C , SRI International


Enzymatic reaction of: 3-hydroxydecanoyl-[acp] dehydrase

Synonyms: 3-hydroxydecanoyl-ACP dehydrase, β-hydroxydecanoyl-ACP dehydrase, 3-hydroxydecanoyl-[acyl carrier protein] dehydrase, β-hydroxydecanoyl thioester dehydrase, 3-hydroxydecanoyl-[acp] dehydratase

EC Number: 2.3.1.86/4.2.1.59

an (R)-3-hydroxydecanoyl-[acp] <=> a trans2-decenoyl-[acp] + H2O

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.

In Pathways: superpathway of fatty acid biosynthesis I (E. coli) , superpathway of unsaturated fatty acids biosynthesis (E. coli) , cis-dodecenoyl biosynthesis


Enzymatic reaction of: 3-hydroxyacyl-[acp] dehydratase (3-hydroxydecanoyl-[acp] dehydrase)

Synonyms: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, β-hydroxyacyl-ACP dehydrase, 3-hydroxyacyl-ACP dehydrase

EC Number: 2.3.1.86/4.2.1.59

a (3R)-3-hydroxyacyl-[acyl-carrier protein] <=> a trans-2-enoyl-[acyl-carrier protein] + H2O

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.

In Pathways: superpathway of fatty acid biosynthesis I (E. coli) , fatty acid elongation -- saturated

Inhibitors (Unknown Mechanism): 3-decynoyl-N-acetylcysteamine [Cronan88]


Enzymatic reaction of: trans-2-decenoyl-ACP isomerase (3-hydroxydecanoyl-[acp] dehydrase)

Synonyms: trans-2-decenoyl-[acyl-carrier-protein] isomerase

EC Number: 5.3.3.14

a trans2-decenoyl-[acp] <=> a cis3-decenoyl-[acp]

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Guerra90]

In Pathways: superpathway of fatty acid biosynthesis I (E. coli) , superpathway of unsaturated fatty acids biosynthesis (E. coli) , cis-dodecenoyl biosynthesis


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[UniProt10a]
UniProt: Removed;
Chain 2 -> 172
[UniProt09]
UniProt: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase;
Active-Site 71
[UniProt10a]
Extrinsic-Sequence-Variant 76
[UniProt10a]
Alternate sequence: P → L; UniProt: (in allele FABA6; TS);
Extrinsic-Sequence-Variant 102
[UniProt10a]
Alternate sequence: G → D; UniProt: (in allele FABA2; TS);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b0954 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10273; confirmed by SwissProt match.


References

Annand93: Annand RR, Kozlowski JF, Davisson V J, Schwab JM (1993). "Mechanism-based inactivation of Escherichia coli .beta.-hydroxydecanoyl thiol ester dehydrase: assignment of the imidazole nitrogen-15 NMR resonances and determination of the structure of the alkylated histidine." Journal of the American Chemical Society 115(3);1088-1094.

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

Brock67: Brock DJ, Kass LR, Bloch K (1967). "Beta-hydroxydecanoyl thioester dehydrase. II. Mode of action." J Biol Chem 242(19);4432-40. PMID: 4863740

Cao10: Cao Y, Yang J, Xian M, Xu X, Liu W (2010). "Increasing unsaturated fatty acid contents in Escherichia coli by coexpression of three different genes." Appl Microbiol Biotechnol 87(1);271-80. PMID: 20135119

Clark83: Clark DP, DeMendoza D, Polacco ML, Cronan JE (1983). "Beta-hydroxydecanoyl thio ester dehydrase does not catalyze a rate-limiting step in Escherichia coli unsaturated fatty acid synthesis." Biochemistry 1983;22(25);5897-902. PMID: 6362720

Cronan72: Cronan JE, Silbert DF, Wulff DL (1972). "Mapping of the fabA locus for unsaturated fatty acid biosynthesis in Escherichia coli." J Bacteriol 112(1);206-11. PMID: 4562395

Cronan73: Cronan JE, Gelmann EP (1973). "An estimate of the minimum amount of unsaturated fatty acid required for growth of Escherichia coli." J Biol Chem 248(4);1188-95. PMID: 4568811

Cronan88: Cronan JE, Li WB, Coleman R, Narasimhan M, de Mendoza D, Schwab JM (1988). "Derived amino acid sequence and identification of active site residues of Escherichia coli beta-hydroxydecanoyl thioester dehydrase." J Biol Chem 1988;263(10);4641-6. PMID: 2832401

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

ECOSAL: "Escherichia coli and Salmonella: Cellular and Molecular Biology." Online edition.

Endo70: Endo K, Helmkamp GM, Bloch K (1970). "Mode of inhibition of beta-hydroxydecanoyl thioester dehydrase by 3-decynoyl-N-acetylcysteamine." J Biol Chem 245(17);4293-6. PMID: 5498414

Feng09: Feng Y, Cronan JE (2009). "Escherichia coli unsaturated fatty acid synthesis: complex transcription of the fabA gene and in vivo identification of the essential reaction catalyzed by FabB." J Biol Chem 284(43);29526-35. PMID: 19679654

Feng11: Feng Y, Cronan JE (2011). "Complex binding of the FabR repressor of bacterial unsaturated fatty acid biosynthesis to its cognate promoters." Mol Microbiol 80(1);195-218. PMID: 21276098

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."

Guerra90: Guerra DJ, Browse JA (1990). "Escherichia coli beta-hydroxydecanoyl thioester dehydrase reacts with native C10 acyl-acyl-carrier proteins of plant and bacterial origin." Arch Biochem Biophys 280(2);336-45. PMID: 2195995

Heath96: Heath RJ, Rock CO (1996). "Roles of the FabA and FabZ beta-hydroxyacyl-acyl carrier protein dehydratases in Escherichia coli fatty acid biosynthesis." J Biol Chem 1996;271(44);27795-801. PMID: 8910376

Helmkamp68: Helmkamp GM, Brock DJ, Bloch K (1968). "Beta-hydroxydecanoly thioester dehydrase. Specificity of substrates and acetylenic inhibitors." J Biol Chem 243(12);3229-31. PMID: 4872868

Helmkamp69: Helmkamp GM, Bloch K (1969). "Beta-hydroxydecanoyl thioester dehydrase. Studies on molecular structure and active site." J Biol Chem 244(21);6014-22. PMID: 4900506

Henry92: Henry MF, Cronan JE (1992). "A new mechanism of transcriptional regulation: release of an activator triggered by small molecule binding." Cell 1992;70(4);671-9. PMID: 1505031

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

Ishikawa12: Ishikawa F, Haushalter RW, Burkart MD (2012). "Dehydratase-specific probes for fatty acid and polyketide synthases." J Am Chem Soc 134(2);769-72. PMID: 22188524

Kass67: Kass LR, Brock DJ, Bloch K (1967). "Beta-hydroxydecanoyl thioester dehydrase. I. Purification and properties." J Biol Chem 242(19);4418-31. PMID: 4863739

Leesong96: Leesong M, Henderson BS, Gillig JR, Schwab JM, Smith JL (1996). "Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site." Structure 4(3);253-64. PMID: 8805534

Magnuson93: Magnuson K, Jackowski S, Rock CO, Cronan JE (1993). "Regulation of fatty acid biosynthesis in Escherichia coli." Microbiol Rev 1993;57(3);522-42. PMID: 8246839

Matsuo92: Matsuo M, Hamato N, Takano R, Kamei-Hayashi K, Yasuda-Kamatani Y, Nomoto K, Hara S (1992). "Trypsin inhibitors from bottle gourd (Lagenaria leucantha Rusby var. Depressa Makino) seeds. Purification and amino acid sequences." Biochim Biophys Acta 1120(2);187-92. PMID: 1562585

Morisaki72: Morisaki M, Bloch K (1972). "On the mode of interaction of -hydroxydecanoyl thioester dehydrase with allenic acid derivatives." Biochemistry 11(3);309-14. PMID: 5059115

NORRIS64: NORRIS AT, MATSUMURA S, BLOCH K (1964). "FATTY ACID SYNTHETASE AND BETA-HYDROXYDECANOYL COENZYME A DEHYDRASE FROM ESCHERICHIA COLI." J Biol Chem 239;3653-62. PMID: 14257590

Nunn83: Nunn WD, Giffin K, Clark D, Cronan JE (1983). "Role for fadR in unsaturated fatty acid biosynthesis in Escherichia coli." J Bacteriol 154(2);554-60. PMID: 6341354

Saito95: Saito K, Hamajima A, Ohkuma M, Murakoshi I, Ohmori S, Kawaguchi A, Teeri TH, Cronan JE (1995). "Expression of the Escherichia coli fabA gene encoding beta-hydroxydecanoyl thioester dehydrase and transport to chloroplasts in transgenic tobacco." Transgenic Res 1995;4(1);60-9. PMID: 7881463

Schwab84: Schwab JM, Klassen JB (1984). "Steric course of the allylic rearrangement catalyzed by .beta.-hydroxydecanoylthioester dehydrase. Mechanistic implications." Journal of the American Chemical Society 106(23);7217-7227.

Schwab84a: Schwab JM, Klassen JB (1984). "?-Hydroxydecanoylthioester dehydrase. Steric course at substrate C-2 and overall steric course of the enzyme?catalysed allylic rearrangement." Journal of the Chemical Society, Chemical Communications (5);298-NIL.

Schwab84b: Schwab JM, Klassen JB (1984). "?-Hydroxydecanoylthioester dehydraes. Steric course at substrate C?4 in the enzyme?catalysed allylic rearrangement." Journal of the Chemical Society, Chemical Communications (5);296-NIL.

Schwab86: Schwab JM, Klassen JB, Habib A (1986). "Stereochemical course of the hydration reaction catalysed by ?-hydroxydecanoylthioester dehydrase." Journal of the Chemical Society, Chemical Communications (4);357-NIL.

Sharma90: Sharma A, Henderson BS, Schwab JM, Smith JL (1990). "Crystallization and preliminary X-ray analysis of beta-hydroxydecanoyl thiol ester dehydrase from Escherichia coli." J Biol Chem 1990;265(9);5110-2. PMID: 2180957

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

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

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Wang04a: Wang H, Cronan JE (2004). "Functional replacement of the FabA and FabB proteins of Escherichia coli fatty acid synthesis by Enterococcus faecalis FabZ and FabF homologues." J Biol Chem 279(33);34489-95. PMID: 15194690

White05: White SW, Zheng J, Zhang YM, Rock (2005). "The structural biology of type II fatty acid biosynthesis." Annu Rev Biochem 74;791-831. PMID: 15952903

Other References Related to Gene Regulation

DiRusso99: DiRusso CC, Black PN, Weimar JD (1999). "Molecular inroads into the regulation and metabolism of fatty acids, lessons from bacteria." Prog Lipid Res 38(2);129-97. PMID: 10396600

Gui96: Gui L, Sunnarborg A, LaPorte DC (1996). "Regulated expression of a repressor protein: FadR activates iclR." J Bacteriol 1996;178(15);4704-9. PMID: 8755903

McCue01: McCue L, Thompson W, Carmack C, Ryan MP, Liu JS, Derbyshire V, Lawrence CE (2001). "Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes." Nucleic Acids Res 2001;29(3);774-82. PMID: 11160901

Zhang02a: Zhang YM, Marrakchi H, Rock CO (2002). "The FabR (YijC) transcription factor regulates unsaturated fatty acid biosynthesis in Escherichia coli." J Biol Chem 2002;277(18);15558-65. PMID: 11859088


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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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