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Escherichia coli K-12 substr. MG1655 Protein: anaerobic fatty acid oxidation complex

Subunit composition of anaerobic fatty acid oxidation complex = [(FadJ)2][(FadI)2]
         FadJ component of anaerobic fatty acid oxidation complex = (FadJ)2
                 FadJ monomer = FadJ
         Fad I component of anaerobic fatty acid oxidation complex = (FadI)2
                 FadI monomer = FadI

Summary:
During anaerobic beta-oxidation of fatty acids FadI, FadJ, and FadK serve functions parallel to those of FadA, FadB, and FadD in the aerobic pathway [Campbell03a].

Gene-Reaction Schematic

Gene-Reaction Schematic

Instance reaction of [a cis-3-enoyl-CoA ↔ a trans-2-enoyl-CoA] (5.3.3.8):
i2: 3-cis-dodecenoyl-CoA = trans-dodec-2-enoyl-CoA (5.3.3.8)

Instance reaction of [a (3S)-3-hydroxyacyl-CoA + NAD+ → a 3-oxoacyl-CoA + NADH + H+] (1.1.1.35):
i1: 3-hydroxy-5-cis-tetradecenoyl-CoA + NAD+ = 3-keto-5-cis-tetradecenoyl-CoA + NADH + H+ (1.1.1.211)


Component enzyme of anaerobic fatty acid oxidation complex : FadJ component of anaerobic fatty acid oxidation complex

Synonyms: yfcX

Gene: fadJ Accession Numbers: G7212 (EcoCyc), b2341, ECK2335

Locations: cytosol

Subunit composition of FadJ component of anaerobic fatty acid oxidation complex = [FadJ]2
         FadJ monomer = FadJ

Map Position: [2,455,037 <- 2,457,181] (52.91 centisomes, 190°)
Length: 2145 bp / 714 aa

Molecular Weight of Polypeptide: 77.072 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred by computational analysisGO:0006629 - lipid metabolic process [UniProtGOA11a]
Inferred by computational analysisGO:0006631 - fatty acid metabolic process [UniProtGOA11a, GOA06, GOA01a]
Inferred by computational analysisGO:0006635 - fatty acid beta-oxidation [UniProtGOA12, GOA01a]
Inferred by computational analysisGO:0008152 - metabolic process [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016042 - lipid catabolic process [UniProtGOA11a, GOA06]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred by computational analysisGO:0003824 - catalytic activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0003857 - 3-hydroxyacyl-CoA dehydrogenase activity [GOA06, GOA01, GOA01a]
Inferred by computational analysisGO:0004300 - enoyl-CoA hydratase activity [GOA06, GOA01, GOA01a]
Inferred by computational analysisGO:0008692 - 3-hydroxybutyryl-CoA epimerase activity [GOA06, GOA01, GOA01a]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016829 - lyase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016853 - isomerase activity [UniProtGOA11a]
Inferred by computational analysisGO:0051287 - NAD binding [GOA01a]
Cellular Component:
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06]
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolismcarbon utilizationfatty acids

Unification Links: DIP:DIP-11990N, EcoliWiki:b2341, ModBase:P77399, Protein Model Portal:P77399, RefSeq:NP_416843, SMR:P77399, UniProt:P77399

Relationship Links: InterPro:IN-FAMILY:IPR001753, InterPro:IN-FAMILY:IPR006108, InterPro:IN-FAMILY:IPR006176, InterPro:IN-FAMILY:IPR006180, InterPro:IN-FAMILY:IPR008927, InterPro:IN-FAMILY:IPR012802, InterPro:IN-FAMILY:IPR013328, InterPro:IN-FAMILY:IPR016040, InterPro:IN-FAMILY:IPR029045, Pfam:IN-FAMILY:PF00378, Pfam:IN-FAMILY:PF00725, Pfam:IN-FAMILY:PF02737, Prosite:IN-FAMILY:PS00067

Catalyzes:
a (3S)-3-hydroxyacyl-CoA ← a trans-2-enoyl-CoA + H2O,
a (3R)-3-hydroxyacyl-CoA ↔ a (3S)-3-hydroxyacyl-CoA,
a cis-3-enoyl-CoA ↔ a trans-2-enoyl-CoA,
a (3S)-3-hydroxyacyl-CoA + NAD+ → a 3-oxoacyl-CoA + NADH + H+

Summary:
During anaerobic beta-oxidation of fatty acids FadI, FadJ, and FadK serve functions parallel to those of FadA, FadB, and FadD in the aerobic pathway [Campbell03a].

FadJ has 34% identity to FadB and, in a fadB mutant background, FadJ is essential for processing of long-chain fatty acids to medium-chain polyhydroxyalkanoates (PHAMCL) [Snell02]. Overproduced protein exhibits enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase activity [Snell02]. A strain producing FadJ and FadI from a plasmid exhibits thiolase activity with beta-ketyoacyl-CoAs of 6 to 12 carbon units but not with acetoacetyl-CoA [Snell02]. FadJ and YfcY copurify over a gel filtration column [Snell02].

Conservation of enoyl-CoA hydratase, 3-hydroxyacyl-CoA epimerase, and 3-hydroxyacyl-CoA dehydrogenase active site residues is observed [Snell02].

FadJ and FadI exhibit partial functional redundancy with FadA and FadB under aerobic conditions and the two complexes are proposed to increase efficiency of the process by favoring substrates of different chain length [Campbell03a].

Regulation has been described [Campbell03a]. FadR represses transcription of yfcYX in the presence of oxygen [Campbell03a]. Transcription of fadJ is induced upon biofilm formation compared to planktonic growth in both exponential and stationary phase. Induction of expression was found to be independent of the presence of the F plasmid [Beloin04].

A fadJ mutant is impaired in biofilm formation [Beloin04].

Citations: [Serres01]

Essentiality data for fadJ knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Component enzyme of anaerobic fatty acid oxidation complex : Fad I component of anaerobic fatty acid oxidation complex

Synonyms: yfcY

Gene: fadI Accession Numbers: G7213 (EcoCyc), b2342, ECK2336

Locations: cytosol

Subunit composition of Fad I component of anaerobic fatty acid oxidation complex = [FadI]2
         FadI monomer = FadI

Map Position: [2,457,181 <- 2,458,491] (52.96 centisomes, 191°)
Length: 1311 bp / 436 aa

Molecular Weight of Polypeptide: 46.531 kD (from nucleotide sequence)


GO Terms:
Biological Process:
Inferred from experimentGO:0033542 - fatty acid beta-oxidation, unsaturated, even number [Campbell03a]
Inferred by computational analysisGO:0006629 - lipid metabolic process [UniProtGOA11a]
Inferred by computational analysisGO:0006631 - fatty acid metabolic process [UniProtGOA11a, GOA06, GOA01a]
Inferred by computational analysisGO:0006635 - fatty acid beta-oxidation [UniProtGOA12]
Inferred by computational analysisGO:0008152 - metabolic process [GOA01a]
Inferred by computational analysisGO:0016042 - lipid catabolic process [UniProtGOA11a, GOA06, GOA01a]
Molecular Function:
Inferred from experimentGO:0003857 - 3-hydroxyacyl-CoA dehydrogenase activity [Snell02]
Inferred from experimentInferred by computational analysisGO:0003988 - acetyl-CoA C-acyltransferase activity [GOA06, GOA01, Snell02]
Inferred from experimentGO:0004300 - enoyl-CoA hydratase activity [Snell02]
Inferred by computational analysisGO:0003824 - catalytic activity [GOA01a]
Inferred by computational analysisGO:0016740 - transferase activity [UniProtGOA11a]
Inferred by computational analysisGO:0016746 - transferase activity, transferring acyl groups [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016747 - transferase activity, transferring acyl groups other than amino-acyl groups [GOA01a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a, Snell02]
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08]

MultiFun Terms: metabolismcarbon utilizationfatty acids

Unification Links: DIP:DIP-11991N, EcoliWiki:b2342, ModBase:P76503, Pride:P76503, Protein Model Portal:P76503, RefSeq:NP_416844, SMR:P76503, Swiss-Model:P76503, UniProt:P76503

Relationship Links: InterPro:IN-FAMILY:IPR002155, InterPro:IN-FAMILY:IPR012806, InterPro:IN-FAMILY:IPR016039, InterPro:IN-FAMILY:IPR020610, InterPro:IN-FAMILY:IPR020613, InterPro:IN-FAMILY:IPR020615, InterPro:IN-FAMILY:IPR020616, InterPro:IN-FAMILY:IPR020617, Panther:IN-FAMILY:PTHR18919, Pfam:IN-FAMILY:PF00108, Pfam:IN-FAMILY:PF02803, Prosite:IN-FAMILY:PS00098, Prosite:IN-FAMILY:PS00099, Prosite:IN-FAMILY:PS00737

Catalyzes:
a 2,3,4-saturated fatty acyl CoA + acetyl-CoA ← a 3-oxoacyl-CoA + coenzyme A

Summary:
During anaerobic beta-oxidation of fatty acids FadI, FadJ, and FadK serve functions parallel to those of FadA, FadB, and FadD in the aerobic pathway [Campbell03a].

FadJ and FadI exhibit partial functional redundancy with FadA and FadB under aerobic conditions and the two complexes are proposed to increase efficiency of the process by favoring substrates of different chain length [Campbell03a].

A strain producing FadJ and FadI from a plasmid exhibits thiolase activity with beta-ketyoacyl-CoAs of 6 to 12 carbon units but not with acetoacetyl-CoA [Snell02]. FadJ and FadI copurify over a gel filtration column [Snell02].

Regulation has been described [Campbell03a]. FadR represses transcription of yfcYX in the presence of oxygen [Campbell03a].

Essentiality data for fadI knockouts:

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enrichedYes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB LennoxYes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerolYes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucoseYes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

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

Beloin04: Beloin C, Valle J, Latour-Lambert P, Faure P, Kzreminski M, Balestrino D, Haagensen JA, Molin S, Prensier G, Arbeille B, Ghigo JM (2004). "Global impact of mature biofilm lifestyle on Escherichia coli K-12 gene expression." Mol Microbiol 51(3);659-74. PMID: 14731270

Campbell03a: Campbell JW, Morgan-Kiss RM, E Cronan J (2003). "A new Escherichia coli metabolic competency: growth on fatty acids by a novel anaerobic beta-oxidation pathway." Mol Microbiol 47(3);793-805. PMID: 12535077

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."

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

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

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

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

Snell02: Snell KD, Feng F, Zhong L, Martin D, Madison LL (2002). "YfcX enables medium-chain-length poly(3-hydroxyalkanoate) formation from fatty acids in recombinant Escherichia coli fadB strains." J Bacteriol 184(20);5696-705. PMID: 12270828

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

UniProtGOA11a: 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."


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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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