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Escherichia coli K-12 substr. MG1655 Polypeptide: formate dehydrogenase-O, γ subunit



Gene: fdoI Accession Numbers: EG11856 (EcoCyc), b3892, ECK3885

Regulation Summary Diagram: ?

Regulation summary diagram for fdoI

Component of: formate dehydrogenase-O (extended summary available)

Summary:
fdoI encodes the γ subunit of formate dehydrogenase O. It has 45% amino acid identity (over an alignment of 156 residues) with the heme b binding, γ subunit (FdnI) of formate dehydrogenase-N [Plunkett93].

Both the N- and C-terminus of FdoI appear to be located in the cytoplasm and it is predicted to have 4 transmembrane regions [Benoit98].

Locations: inner membrane

Map Position: [4,079,248 <- 4,079,883] (87.92 centisomes, 317°)
Length: 636 bp / 211 aa

Molecular Weight of Polypeptide: 24.606 kD (from nucleotide sequence)

pI: 10.3

Isozyme Sequence Similarity:
formate dehydrogenase N, γ subunit: YES

Unification Links: ASAP:ABE-0012705 , CGSC:33991 , EchoBASE:EB1802 , EcoGene:EG11856 , EcoliWiki:b3892 , ModBase:P0AEL0 , OU-Microarray:b3892 , PortEco:fdoI , PR:PRO_000022586 , Protein Model Portal:P0AEL0 , RefSeq:NP_418328 , RegulonDB:EG11856 , SMR:P0AEL0 , String:511145.b3892 , Swiss-Model:P0AEL0 , UniProt:P0AEL0

Relationship Links: InterPro:IN-FAMILY:IPR006471 , InterPro:IN-FAMILY:IPR016174 , Panther:IN-FAMILY:PTHR30074:SF2 , Pfam:IN-FAMILY:PF00033

Reactions known to consume the compound:

Not in pathways:
a ubiquinol-8 oxidoreductase + a b-type cytochrome → a ubiquinone-8 oxidoreductase + a reduced b-type cytochrome
a b-type cytochrome + a menaquinone oxidoreductase (demethylmenaquinol) → a reduced b-type cytochrome + a menaquinone oxidoreductase (demethylmenaquinone)
a b-type cytochrome + a menaquinone oxidoreductase (menaquinol-8) → a reduced b-type cytochrome + a menaquinone oxidoreductase (menaquinone-8)
a reduced b-type cytochrome + a b-type cytochromea b-type cytochrome + a reduced cytochrome o

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0009061 - anaerobic respiration Inferred from experiment [Sawers91, Abaibou95]
GO:0015944 - formate oxidation Inferred from experiment [Abaibou95]
GO:0045333 - cellular respiration Inferred from experiment Inferred by computational analysis [GOA01a, Abaibou95]
GO:0022904 - respiratory electron transport chain Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008863 - formate dehydrogenase (NAD+) activity Inferred by computational analysis [GOA01a]
GO:0020037 - heme binding Inferred by computational analysis [Sawers94]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
GO:0005887 - integral component of plasma membrane Inferred from experiment Inferred by computational analysis [Benoit98]
GO:0009326 - formate dehydrogenase complex Inferred from experiment Inferred by computational analysis [GOA01a, Abaibou95]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: cell structure membrane
metabolism biosynthesis of macromolecules (cellular constituents) large molecule carriers cytochromes
metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron donors

Essentiality data for fdoI 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]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 03-Dec-2014 by Mackie A , Macquarie University


Subunit of: formate dehydrogenase-O

Synonyms: FDH-O, FDH-Z, formate:quinone oxidoreductase O, formate:quinone oxidoreductase Z

Subunit composition of formate dehydrogenase-O = [FdoG][FdoH][FdoI]
         formate dehydrogenase-O, α subunit = FdoG (summary available)
         formate dehydrogenase-O, β subunit = FdoH (summary available)
         formate dehydrogenase-O, γ subunit = FdoI (summary available)

Summary:
fdoGHI encodes formate dehydrogenase O (FDH-O) - a respiratory molybdoenzyme that catalyses the oxidation of formate to carbon dioxide, donating electrons to the membrane soluble quinone pool for the reduction of nitrate. FDH-O and nitrate reductase Z participate in a formate to nitrate electron transport pathway that is active when cells are shifted from aerobic to anaerobic conditions. The pathway operates with either menaquinone or ubiquinone [Sawers91, Pommier92]

FDH-O appears to be expressed constitutively; unlike formate dehydrogenase N (FDH-N), it is not regulated by Fnr or NarL [Pommier92]. Expression of FDH-O is increased under aerobic conditions; under anaerobic conditions, nitrate stimulates expression slightly; the global regulators H-NS and CRP may play a role in regulation of FDH-O expression. FDH-O may contribute to the cells ability to rapidly adapt to anaerobiosis while levels of FDH-N are still insufficient [Sawers91, Abaibou95].

FDH-O is a heterotrimeric complex consisting of an α (FdoG), a β (FdoH) and a γ (FdoI) subunit - it shares extensive sequence similarity and immunological properties with the anaerobically expressed FDH-N [Pommier92, Abaibou95, Plunkett93].

The presence of a formate oxidase supercomplex consisting of cytochromes bo and bd-1 plus formate dehydrogenase-O in a 1:1:1 stoichiometry has been suggested by electrophoretic and spectrometric analyses [Sousa11].

E. coli K-12 contains two other formate dehydrogenases - the anaerobically expressed formate dehydrogenase-N complex and formate dehydrogenase-H - a component of the fermentative formate-hydrogenlyase complex.

Reviews: [Sawers94]

Locations: membrane

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Abaibou95, Sawers91]
GO:0015944 - formate oxidation Inferred from experiment [Abaibou95, Pommier92]
GO:0022904 - respiratory electron transport chain Inferred from experiment [Pommier92]
GO:0045333 - cellular respiration Inferred from experiment [Abaibou95]
Molecular Function: GO:0008430 - selenium binding Inferred from experiment [Sawers91]
GO:0036397 - formate dehydrogenase (quinone) activity Inferred from experiment [Pommier92]
GO:0043546 - molybdopterin cofactor binding Inferred from experiment [Pommier92]
Cellular Component: GO:0009326 - formate dehydrogenase complex Inferred from experiment [Abaibou95, Pommier92]
GO:0016020 - membrane Inferred from experiment [Pommier92]

Credits:
Revised 03-Dec-2014 by Mackie A , Macquarie University
Last-Curated ? 03-Dec-2014 by Mackie A , Macquarie University


Enzymatic reaction of: formate dehydrogenase-O

EC Number: 1.1.5.6

Transport reaction diagram for formate dehydrogenase-O

In Pathways: nitrate reduction III (dissimilatory) , formate to dimethyl sulfoxide electron transfer , formate to trimethylamine N-oxide electron transfer , formate to nitrite electron transfer

Cofactors or Prosthetic Groups: bis(guanylyl molybdopterin cofactor) [Pommier92]


Sequence Features

Protein sequence of formate dehydrogenase-O, gamma subunit with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 18
[UniProt10a]
UniProt: Iron (heme B 1 axial ligand); Non-Experimental Qualifier: by similarity;
Transmembrane-Region 18 -> 32
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Transmembrane-Region 54 -> 72
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Metal-Binding-Site 57
[UniProt10a]
UniProt: Iron (heme B 2 axial ligand); Non-Experimental Qualifier: by similarity;
Transmembrane-Region 113 -> 130
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Transmembrane-Region 152 -> 170
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: probable;
Metal-Binding-Site 153
[UniProt10a]
UniProt: Iron (heme B 2 axial ligand); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 167
[UniProt10a]
UniProt: Iron (heme B 1 axial ligand); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b3892 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11856; confirmed by SwissProt match.


References

Abaibou95: Abaibou H, Pommier J, Benoit S, Giordano G, Mandrand-Berthelot MA (1995). "Expression and characterization of the Escherichia coli fdo locus and a possible physiological role for aerobic formate dehydrogenase." J Bacteriol 177(24);7141-9. PMID: 8522521

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

Benoit98: Benoit S, Abaibou H, Mandrand-Berthelot MA (1998). "Topological analysis of the aerobic membrane-bound formate dehydrogenase of Escherichia coli." J Bacteriol 1998;180(24);6625-34. PMID: 9852007

Daley05: Daley DO, Rapp M, Granseth E, Melen K, Drew D, von Heijne G (2005). "Global topology analysis of the Escherichia coli inner membrane proteome." Science 308(5726);1321-3. PMID: 15919996

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

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

Khil02: Khil PP, Camerini-Otero RD (2002). "Over 1000 genes are involved in the DNA damage response of Escherichia coli." Mol Microbiol 44(1);89-105. PMID: 11967071

Plunkett93: Plunkett G, Burland V, Daniels DL, Blattner FR (1993). "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Nucleic Acids Res 1993;21(15);3391-8. PMID: 8346018

Pommier92: Pommier J, Mandrand MA, Holt SE, Boxer DH, Giordano G (1992). "A second phenazine methosulphate-linked formate dehydrogenase isoenzyme in Escherichia coli." Biochim Biophys Acta 1107(2);305-13. PMID: 1504073

Sawers91: Sawers G, Heider J, Zehelein E, Bock A (1991). "Expression and operon structure of the sel genes of Escherichia coli and identification of a third selenium-containing formate dehydrogenase isoenzyme." J Bacteriol 1991;173(16);4983-93. PMID: 1650339

Sawers94: Sawers G (1994). "The hydrogenases and formate dehydrogenases of Escherichia coli." Antonie Van Leeuwenhoek 1994;66(1-3);57-88. PMID: 7747941

Sousa11: Sousa PM, Silva ST, Hood BL, Charro N, Carita JN, Vaz F, Penque D, Conrads TP, Melo AM (2011). "Supramolecular organizations in the aerobic respiratory chain of Escherichia coli." Biochimie 93(3);418-25. PMID: 21040753

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 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."

Other References Related to Gene Regulation

Campagne14: Campagne S, Marsh ME, Capitani G, Vorholt JA, Allain FH (2014). "Structural basis for -10 promoter element melting by environmentally induced sigma factors." Nat Struct Mol Biol 21(3);269-76. PMID: 24531660

Trotter11: Trotter EW, Rolfe MD, Hounslow AM, Craven CJ, Williamson MP, Sanguinetti G, Poole RK, Green J (2011). "Reprogramming of Escherichia coli K-12 metabolism during the initial phase of transition from an anaerobic to a micro-aerobic environment." PLoS One 6(9);e25501. PMID: 21980479


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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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