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Escherichia coli K-12 substr. MG1655 Polypeptide: predicted electron transfer flavoprotein, NAD/FAD-binding domain and ETFP adenine nucleotide-binding domain-like



Gene: fixB Accession Numbers: EG11563 (EcoCyc), b0042, ECK0043

Synonyms: yaaR

Regulation Summary Diagram: ?

Summary:
FixA and FixB are required for anaerobic carnitine reduction and are proposed to act in the transfer of electrons to crotonobetainyl-CoA reductase (CaiA) [Walt02]. FixA and FixB have similarity to mammalian electron transfer flavoprotein subunits [Eichler95] (ETF-β and α families, respectively) [Tsai95] and were predicted to play an electron transport role in E. coli based on sequence similarity [Eichler95].

fixA, fixB, ydiQ, ydiR, ygcR, and ygcQ form a subsystem based on genome context methods, and may represent a previously uncharacterized electron transfer pathway [Ferrer11].

A fixA or fixB mutant exhibits a defect in anaerobic reduction of carnitine to γ-butyrobetaine [Walt02].

The cai and fix operons are divergently transcribed in a coordinated fashion [Buchet98]. Transcription is activated under conditions of anaerobiosis plus crotonobetaine or L-carnitine [Eichler95].

Map Position: [43,188 -> 44,129] (0.93 centisomes)
Length: 942 bp / 313 aa

Molecular Weight of Polypeptide: 33.513 kD (from nucleotide sequence), 33 kD (experimental) [Eichler95 ]

Unification Links: ASAP:ABE-0000147 , DIP:DIP-9621N , EchoBASE:EB1524 , EcoGene:EG11563 , EcoliWiki:b0042 , Mint:MINT-1240082 , ModBase:P31574 , OU-Microarray:b0042 , PortEco:fixB , PR:PRO_000022629 , Protein Model Portal:P31574 , RefSeq:NP_414584 , RegulonDB:EG11563 , SMR:P31574 , String:511145.b0042 , UniProt:P31574

Relationship Links: InterPro:IN-FAMILY:IPR001308 , InterPro:IN-FAMILY:IPR014729 , InterPro:IN-FAMILY:IPR014730 , InterPro:IN-FAMILY:IPR014731 , InterPro:IN-FAMILY:IPR018206 , InterPro:IN-FAMILY:IPR023461 , Pfam:IN-FAMILY:PF00766 , Pfam:IN-FAMILY:PF01012 , Prosite:IN-FAMILY:PS00696 , Smart:IN-FAMILY:SM00893

In Paralogous Gene Group: 16 (3 members)

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009437 - carnitine metabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA06, GOA01, Walt02]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA06]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01]
GO:0050660 - flavin adenine dinucleotide binding Inferred by computational analysis [GOA01]

MultiFun Terms: metabolism energy production/transport

Essentiality data for fixB 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 ? 05-Jun-2014 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 255 -> 283
[UniProt10a]
UniProt: FAD; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0042 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11563; confirmed by SwissProt match.


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

Buchet98: Buchet A, Eichler K, Mandrand-Berthelot MA (1998). "Regulation of the carnitine pathway in Escherichia coli: investigation of the cai-fix divergent promoter region." J Bacteriol 1998;180(10);2599-608. PMID: 9573142

Eichler95: Eichler K, Buchet A, Bourgis F, Kleber HP, Mandrand-Berthelot MA (1995). "The fix Escherichia coli region contains four genes related to carnitine metabolism." J Basic Microbiol 35(4);217-27. PMID: 7473063

Ferrer11: Ferrer L, Shearer AG, Karp PD (2011). "Discovering novel subsystems using comparative genomics." Bioinformatics 27(18);2478-85. PMID: 21775308

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, 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."

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

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Tsai95: Tsai MH, Saier MH (1995). "Phylogenetic characterization of the ubiquitous electron transfer flavoprotein families ETF-alpha and ETF-beta." Res Microbiol 146(5);397-404. PMID: 8525056

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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."

Walt02: Walt A, Kahn ML (2002). "The fixA and fixB genes are necessary for anaerobic carnitine reduction in Escherichia coli." J Bacteriol 184(14);4044-7. PMID: 12081978

Other References Related to Gene Regulation

Buchet99: Buchet A, Nasser W, Eichler K, Mandrand-Berthelot MA (1999). "Positive co-regulation of the Escherichia coli carnitine pathway cai and fix operons by CRP and the CaiF activator." Mol Microbiol 1999;34(3);562-75. PMID: 10564497

Constantinidou06: Constantinidou C, Hobman JL, Griffiths L, Patel MD, Penn CW, Cole JA, Overton TW (2006). "A reassessment of the FNR regulon and transcriptomic analysis of the effects of nitrate, nitrite, NarXL, and NarQP as Escherichia coli K12 adapts from aerobic to anaerobic growth." J Biol Chem 281(8);4802-15. PMID: 16377617

Eichler96: Eichler K, Buchet A, Lemke R, Kleber HP, Mandrand-Berthelot MA (1996). "Identification and characterization of the caiF gene encoding a potential transcriptional activator of carnitine metabolism in Escherichia coli." J Bacteriol 1996;178(5);1248-57. PMID: 8631699

Salmon03: Salmon K, Hung SP, Mekjian K, Baldi P, Hatfield GW, Gunsalus RP (2003). "Global gene expression profiling in Escherichia coli K12. The effects of oxygen availability and FNR." J Biol Chem 278(32);29837-55. PMID: 12754220


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 Nov 24, 2014, biocyc13.