Escherichia coli K-12 substr. MG1655 Enzyme: malonyl-CoA-ACP transacylase

Gene: fabD Accession Numbers: EG11317 (EcoCyc), b1092, ECK1078

Synonyms: tfpA, tpfA

Regulation Summary Diagram: ?

Regulation summary diagram for fabD

The fabD gene is part of a fatty acid biosynthesis operon and the malonyl-CoA transacylase is part of a multienzyme fatty acid synthase II complex [Verwoert92].

Gene Citations: [Zhang98c, Podkovyrov95, Zhang96c, Podkovyrov96]

Locations: cytosol

Map Position: [1,148,951 -> 1,149,880] (24.76 centisomes, 89°)
Length: 930 bp / 309 aa

Molecular Weight of Polypeptide: 32.417 kD (from nucleotide sequence)

pI: 5.12

Unification Links: ASAP:ABE-0003698 , DIP:DIP-47923N , EchoBASE:EB1293 , EcoGene:EG11317 , EcoliWiki:b1092 , OU-Microarray:b1092 , PortEco:fabD , PR:PRO_000022561 , Pride:P0AAI9 , Protein Model Portal:P0AAI9 , RefSeq:NP_415610 , RegulonDB:EG11317 , SMR:P0AAI9 , String:511145.b1092 , UniProt:P0AAI9

Relationship Links: InterPro:IN-FAMILY:IPR001227 , InterPro:IN-FAMILY:IPR004410 , InterPro:IN-FAMILY:IPR014043 , InterPro:IN-FAMILY:IPR016035 , InterPro:IN-FAMILY:IPR016036 , InterPro:IN-FAMILY:IPR024925 , PDB:Structure:1MLA , PDB:Structure:2G1H , PDB:Structure:2G2O , PDB:Structure:2G2Y , PDB:Structure:2G2Z , Pfam:IN-FAMILY:PF00698

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for fabD

GO Terms:

Biological Process: GO:0006633 - fatty acid biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, Ruch73]
GO:0006629 - lipid metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0006631 - fatty acid metabolic process Inferred by computational analysis [UniProtGOA11]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0004314 - [acyl-carrier-protein] S-malonyltransferase activity Inferred from experiment Inferred by computational analysis [GOA01a, GOA01, Verwoert92]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0016746 - transferase activity, transferring acyl groups Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]

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

Essentiality data for fabD knockouts: ?

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

Enzymatic reaction of: malonyl-CoA-ACP transacylase

Synonyms: malonyl-CoA-acyl carrier protein transacylase, [acyl-carrier-protein]-S-malonyltransferase, S-malonyltransferase, malonyl-CoA:[acyl carrier protein] S-malonyltransferase, malonyl transacylase, malonyl coenzyme A-acyl carrier protein transacylase

EC Number:

a holo-[acyl-carrier protein] + malonyl-CoA <=> a malonyl-[acp] + coenzyme A

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.

In Pathways: superpathway of fatty acid biosynthesis I (E. coli) , superpathway of fatty acid biosynthesis initiation (E. coli) , fatty acid biosynthesis initiation I

Malonyl-CoA-acyl carrier protein transacylase catalyzes one of the early reactions of fatty acid biosynthesis, the transfer of the malonyl group from malonyl-CoA to acyl carrier protein (ACP) to form malonyl-ACP. A malonyl-enzyme intermediate is formed during the reaction. The reaction utilizes a `Ping-Pong Bi Bi' mechanism [Joshi71, Ruch73, Ruch73a].

Inhibitors (Competitive): a malonyl-[acp] [Joshi71, Comment 2] , coenzyme A [Joshi71, Comment 3] , acetyl-CoA [Joshi71, Comment 4]

Inhibitors (Unknown Mechanism): N-ethylmaleimide [Ruch73] , iodoacetamide [Ruch73] , p-chloromercuribenzoate [Ruch73]

Kinetic Parameters:

kcat (sec-1)
[Misra09, BRENDA14]

T(opt): 38 °C [BRENDA14, Williamson66]

pH(opt): 6 [BRENDA14, Ruch73a], 6.5 [BRENDA14, Szafranska02]

Sequence Features

Protein sequence of malonyl-CoA-ACP transacylase with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Pasquali94, Magnuson92, Link97, UniProt12]
UniProt: Removed.
Chain 2 -> 309
UniProt: Malonyl CoA-acyl carrier protein transacylase;
Active-Site 92
Active-Site 201

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


1/26/1998 (pkarp) Merged genes G8000/fabD and EG11317/fabD


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."

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

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.

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

Joshi71: Joshi VC, Wakil SJ (1971). "Studies on the mechanism of fatty acid synthesis. XXVI. Purification and properties of malonyl-coenzyme A--acyl carrier protein transacylase of Escherichia coli." Arch Biochem Biophys 1971;143(2);493-505. PMID: 4934182

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Magnuson92: Magnuson K, Oh W, Larson TJ, Cronan JE (1992). "Cloning and nucleotide sequence of the fabD gene encoding malonyl coenzyme A-acyl carrier protein transacylase of Escherichia coli." FEBS Lett 299(3);262-6. PMID: 1339356

Misra09: Misra A, Surolia N, Surolia A (2009). "Catalysis and mechanism of malonyl transferase activity in type II fatty acid biosynthesis acyl carrier proteins." Mol Biosyst 5(6);651-9. PMID: 19462023

Pasquali94: Pasquali C., Sanchez J.-C., Ravier F., Golaz O., Hughes G.J., Frutiger S., Paquet N., Wilkins M., Appel R.D., Bairoch A., Hochstrasser D.F. (1994). Data submission to UniProtKB on 1994-09.

Podkovyrov95: Podkovyrov S, Larson TJ (1995). "Lipid biosynthetic genes and a ribosomal protein gene are cotranscribed." FEBS Lett 368(3);429-31. PMID: 7635191

Podkovyrov96: Podkovyrov SM, Larson TJ (1996). "Identification of promoter and stringent regulation of transcription of the fabH, fabD and fabG genes encoding fatty acid biosynthetic enzymes of Escherichia coli." Nucleic Acids Res 1996;24(9);1747-52. PMID: 8649995

Ruch73: Ruch FE, Vagelos PR (1973). "The isolation and general properties of Escherichia coli malonyl coenzyme A-acyl carrier protein transacylase." J Biol Chem 1973;248(23);8086-94. PMID: 4584822

Ruch73a: Ruch FE, Vagelos PR (1973). "Characterization of a malonyl-enzyme intermediate and identification of the malonyl binding site in malonyl coenzyme A-acyl carrier protein transacylase of Escherichia coli." J Biol Chem 1973;248(23);8095-106. PMID: 4584823

Szafranska02: Szafranska AE, Hitchman TS, Cox RJ, Crosby J, Simpson TJ (2002). "Kinetic and mechanistic analysis of the malonyl CoA:ACP transacylase from Streptomyces coelicolor indicates a single catalytically competent serine nucleophile at the active site." Biochemistry 41(5);1421-7. PMID: 11814333

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

UniProt12: UniProt Consortium (2012). "UniProt version 2012-02 released on 2012-02-29 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 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."

Verwoert92: Verwoert II, Verbree EC, van der Linden KH, Nijkamp HJ, Stuitje AR (1992). "Cloning, nucleotide sequence, and expression of the Escherichia coli fabD gene, encoding malonyl coenzyme A-acyl carrier protein transacylase." J Bacteriol 1992;174(9);2851-7. PMID: 1314802

Williamson66: Williamson IP, Wakil SJ (1966). "Studies on the mechanism of fatty acid synthesis. XVII. Preparation and general properties of acetyl coenzyme A and malonyl coenzyme A-acyl carrier protein transacylases." J Biol Chem 241(10);2326-32. PMID: 5330116

Zhang96c: Zhang Y, Cronan JE (1996). "Polar allele duplication for transcriptional analysis of consecutive essential genes: application to a cluster of Escherichia coli fatty acid biosynthetic genes." J Bacteriol 1996;178(12);3614-20. PMID: 8655562

Zhang98c: Zhang Y, Cronan JE (1998). "Transcriptional analysis of essential genes of the Escherichia coli fatty acid biosynthesis gene cluster by functional replacement with the analogous Salmonella typhimurium gene cluster." J Bacteriol 180(13);3295-303. PMID: 9642179

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

My13: My L, Rekoske B, Lemke JJ, Viala JP, Gourse RL, Bouveret E (2013). "Transcription of the Escherichia coli Fatty Acid Synthesis Operon fabHDG Is Directly Activated by FadR and Inhibited by ppGpp." J Bacteriol 195(16);3784-95. PMID: 23772072

Tanaka89a: Tanaka Y, Tsujimura A, Fujita N, Isono S, Isono K (1989). "Cloning and analysis of an Escherichia coli operon containing the rpmF gene for ribosomal protein L32 and the gene for a 30-kilodalton protein." J Bacteriol 1989;171(10);5707-12. PMID: 2477362

Thomason15: Thomason MK, Bischler T, Eisenbart SK, Forstner KU, Zhang A, Herbig A, Nieselt K, Sharma CM, Storz G (2015). "Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli." J Bacteriol 197(1);18-28. PMID: 25266388

Zhang12b: Zhang F, Ouellet M, Batth TS, Adams PD, Petzold CJ, Mukhopadhyay A, Keasling JD (2012). "Enhancing fatty acid production by the expression of the regulatory transcription factor FadR." Metab Eng 14(6);653-60. PMID: 23026122

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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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