Escherichia coli K-12 substr. MG1655 Enzyme: 8-amino-7-oxononanoate synthase

Gene: bioF Accession Numbers: EG10121 (EcoCyc), b0776, ECK0765

Regulation Summary Diagram: ?

Regulation summary diagram for bioF

Subunit composition of 8-amino-7-oxononanoate synthase = [BioF]2
         8-amino-7-oxononanoate synthase monomer = BioF

8-Amino-7-oxononanoate synthase catalyzes the decarboxylative condensation of L-alanine and pimeloyl-CoA or pimeloyl-[acp] to form 8-amino-7-oxononanoate [Alexeev98, Lin10], but it has been suggested that pimeloyl-[acp] rather than pimeloyl-CoA is the physiological substrate [Lin10].

Crystal structures of apo- and PLP-bound 8-amino-7-oxononanoate synthase have been solved, providing a framework for understanding the catalytic mechanism [Alexeev98]. Further crystallographic and kinetic studies have provided a detailed view of the mechanism [Webster00].

The N-terminal methionine is removed post-translationally [Alexeev98, Webster00].

Expression of bioF is increased more than 20-fold in a strain containing a ydgG deletion [Herzberg06]. A bioF mutant shows decreased biofilm formation [Herzberg06].

Gene Citations: [Nath82]

Locations: cytosol

Map Position: [809,604 -> 810,758] (17.45 centisomes, 63°)
Length: 1155 bp / 384 aa

Molecular Weight of Polypeptide: 41.594 kD (from nucleotide sequence)

pI: 7.08

Unification Links: ASAP:ABE-0002646 , CGSC:955 , DIP:DIP-6870N , EchoBASE:EB0119 , EcoGene:EG10121 , EcoliWiki:b0776 , ModBase:P12998 , OU-Microarray:b0776 , PortEco:bioF , PR:PRO_000022225 , Pride:P12998 , Protein Model Portal:P12998 , RefSeq:NP_415297 , RegulonDB:EG10121 , SMR:P12998 , String:511145.b0776 , UniProt:P12998

Relationship Links: InterPro:IN-FAMILY:IPR001917 , InterPro:IN-FAMILY:IPR004723 , InterPro:IN-FAMILY:IPR004839 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015422 , InterPro:IN-FAMILY:IPR015424 , InterPro:IN-FAMILY:IPR022834 , PDB:Structure:1BS0 , PDB:Structure:1DJ9 , PDB:Structure:1DJE , PDB:Structure:2G6W , Pfam:IN-FAMILY:PF00155 , Prosite:IN-FAMILY:PS00599

In Paralogous Gene Group: 193 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for bioF

GO Terms:

Biological Process: GO:0009102 - biotin biosynthetic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11, GOA06, GOA01a, Rolfe70]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0009058 - biosynthetic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0008710 - 8-amino-7-oxononanoate synthase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Webster00]
GO:0030170 - pyridoxal phosphate binding Inferred from experiment Inferred by computational analysis [GOA06, GOA01a, Webster00]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism biosynthesis of building blocks cofactors, small molecule carriers biotin

Essentiality data for bioF 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 0.4% glucose No 37 Aerobic 7.2 0.27 No [Patrick07, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Indeterminate 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
No [Feist07, Comment 5]

Last-Curated ? 16-Jan-2007 by Keseler I , SRI International

Enzymatic reaction of: 8-amino-7-oxononanoate synthase

EC Number:

a pimeloyl-[acp] + L-alanine + H+ <=> 8-amino-7-oxononanoate + CO2 + a holo-[acyl-carrier protein]

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 favored in the direction shown.

In Pathways: biotin biosynthesis I , 8-amino-7-oxononanoate biosynthesis I

Enzymatic reaction of: 8-amino-7-oxononanoate synthase

Synonyms: AONS, 7-keto-8-amino-pelargonic acid synthetase, 7-KAP synthetase, 6-carboxyhexanoyl-CoA:L-alanine C-carboxyhexanoyltransferase (decarboxylating)

EC Number:

L-alanine + pimeloyl-CoA + H+ <=> CO2 + 8-amino-7-oxononanoate + coenzyme A

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Note: The enzyme may catalyze this reaction in vitro, but this reaction is not considered to be physiologically relevant.

Alternative Substrates for L-alanine: L-serine [Comment 6 , Eisenberg68 ]

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Comment 7, Eisenberg68]

Inhibitors (Unknown Mechanism): L-cysteine [Eisenberg68, Eisenberg73] , trifluoroalanine [Alexeev06]

Kinetic Parameters:

Km (μM)

Sequence Features

Protein sequence of 8-amino-7-oxononanoate synthase monomer with features indicated

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Webster00, UniProt11]
UniProt: Removed.
Chain 2 -> 384
UniProt: 8-amino-7-oxononanoate synthase;
Amino-Acid-Sites-That-Bind 21
[Webster00, UniProt15]
UniProt: Substrate.
Protein-Segment 108 -> 109
UniProt: Pyridoxal phosphate binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 133
[Webster00, UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 179
[Webster00, UniProt15]
UniProt: Pyridoxal phosphate.
Sequence-Conflict 188 -> 189
UniProt: (in Ref. 2; CAA00968).
Protein-Segment 204 -> 207
UniProt: Pyridoxal phosphate binding; Sequence Annotation Type: region of interest;
Protein-Segment 233 -> 236
UniProt: Pyridoxal phosphate binding; Sequence Annotation Type: region of interest;
N6-pyridoxal-phosphate-Lys-Modification 236
UniProt: N6-(pyridoxal phosphate)lysine.
Amino-Acid-Sites-That-Bind 352
[Webster00, UniProt15]
UniProt: Substrate.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b0776 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10121; confirmed by SwissProt match.


Alexeev06: Alexeev D, Baxter RL, Campopiano DJ, Kerbarh O, Sawyer L, Tomczyk N, Watt R, Webster SP (2006). "Suicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine." Org Biomol Chem 4(7);1209-12. PMID: 16557306

Alexeev98: Alexeev D, Alexeeva M, Baxter RL, Campopiano DJ, Webster SP, Sawyer L (1998). "The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme." J Mol Biol 1998;284(2);401-19. PMID: 9813126

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

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

Eisenberg68: Eisenberg MA, Star C (1968). "Synthesis of 7-oxo-8-aminopelargonic acid, a biotin vitamer, in cell-free extracts of Escherichia coli biotin auxotrophs." J Bacteriol 1968;96(4);1291-7. PMID: 4879561

Eisenberg73: Eisenberg MA (1973). "Biotin: biogenesis, transport, and their regulation." Adv Enzymol Relat Areas Mol Biol 1973;38;317-72. PMID: 4598072

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."

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

Herzberg06: Herzberg M, Kaye IK, Peti W, Wood TK (2006). "YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport." J Bacteriol 188(2);587-98. PMID: 16385049

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

Lin10: Lin S, Hanson RE, Cronan JE (2010). "Biotin synthesis begins by hijacking the fatty acid synthetic pathway." Nat Chem Biol 6(9);682-8. PMID: 20693992

Nath82: Nath SK, Guha A (1982). "Abortive termination of bioBFCD RNA synthesized in vitro from the bioABFCD operon of Escherichia coli K-12." Proc Natl Acad Sci U S A 79(6);1786-90. PMID: 6177001

Patrick07: Patrick WM, Quandt EM, Swartzlander DB, Matsumura I (2007). "Multicopy suppression underpins metabolic evolvability." Mol Biol Evol 24(12);2716-22. PMID: 17884825

Rolfe70: Rolfe B (1970). "Lambda phage transduction of the bio A locus of Escherichia coli." Virology 42(3);643-61. PMID: 4921685

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

UniProt10: 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.

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."

Webster00: Webster SP, Alexeev D, Campopiano DJ, Watt RM, Alexeeva M, Sawyer L, Baxter RL (2000). "Mechanism of 8-amino-7-oxononanoate synthase: spectroscopic, kinetic, and crystallographic studies." Biochemistry 39(3);516-28. PMID: 10642176

Other References Related to Gene Regulation

AbdelHamid07: Abdel-Hamid AM, Cronan JE (2007). "Coordinate expression of the acetyl coenzyme A carboxylase genes, accB and accC, is necessary for normal regulation of biotin synthesis in Escherichia coli." J Bacteriol 189(2);369-76. PMID: 17056747

Cronan89: Cronan JE (1989). "The E. coli bio operon: transcriptional repression by an essential protein modification enzyme." Cell 58(3);427-9. PMID: 2667763

Lin91: Lin KC, Campbell A, Shiuan D (1991). "Binding characteristics of Escherichia coli biotin repressor-operator complex." Biochim Biophys Acta 1090(3);317-25. PMID: 1659455

Otsuka78: Otsuka A, Abelson J (1978). "The regulatory region of the biotin operon in Escherichia coli." Nature 1978;276(5689);689-94. PMID: 366433

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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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