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MetaCyc Transporter: formate dehydrogenase

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

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of formate dehydrogenase = [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: inner membrane

Gene-Reaction Schematic

Gene-Reaction Schematic


GO Terms:
Biological Process:
Inferred from experimentGO:0009061 - anaerobic respiration [Abaibou95, Sawers91]
Inferred from experimentGO:0015944 - formate oxidation [Abaibou95, Pommier92]
Inferred from experimentGO:0022904 - respiratory electron transport chain [Pommier92]
Inferred from experimentGO:0045333 - cellular respiration [Abaibou95]
Molecular Function:
Inferred from experimentGO:0008430 - selenium binding [Sawers91]
Inferred from experimentGO:0036397 - formate dehydrogenase (quinone) activity [Pommier92]
Inferred from experimentGO:0043546 - molybdopterin cofactor binding [Pommier92]
Cellular Component:
Inferred from experimentGO:0005886 - plasma membrane [Pommier92]
Inferred from experimentGO:0009326 - formate dehydrogenase complex [Abaibou95, Pommier92]

Credits:
Revised in EcoCyc 03-Dec-2014 by Mackie A, Macquarie University
Imported from EcoCyc 30-Sep-2015 by Paley S, SRI International


Enzymatic reaction of: formate dehydrogenase

Inferred from experiment

Transport reaction diagram for formate dehydrogenase

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

Credits:
Imported from EcoCyc 30-Sep-2015 by Paley S, SRI International

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


Subunit of formate dehydrogenase: formate dehydrogenase-O, α subunit

Synonyms: FdoG

Gene: fdoG Accession Numbers: EG11858 (MetaCyc), b3894, ECK3887

Locations: periplasm, cytosol, membrane

Sequence Length: 1016 AAs

Molecular Weight: 112.55 kD (from nucleotide sequence)

Molecular Weight: 100.0 kD (experimental) [Pommier92]

pI: 7.8


GO Terms:
Biological Process:
Inferred from experimentGO:0006974 - cellular response to DNA damage stimulus [Khil02]
Inferred from experimentGO:0009061 - anaerobic respiration [Sawers91, Abaibou95]
Inferred from experimentGO:0015944 - formate oxidation [Pommier92, Abaibou95]
Inferred from experimentInferred by computational analysisGO:0045333 - cellular respiration [GOA01a, Abaibou95]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a, GOA01a]
Molecular Function:
Inferred from experimentGO:0005515 - protein binding [Chan10, Chan09, Arifuzzaman06]
Inferred from experimentGO:0036397 - formate dehydrogenase (quinone) activity [Pommier92]
Inferred by computational analysisGO:0003954 - NADH dehydrogenase activity [Gaudet10]
Inferred by computational analysisGO:0008863 - formate dehydrogenase (NAD+) activity [GOA01, GOA01a, Gaudet10]
Inferred by computational analysisGO:0009055 - electron carrier activity [GOA01a, Gaudet10]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0030151 - molybdenum ion binding [GOA01a, Gaudet10]
Inferred by computational analysisGO:0043546 - molybdopterin cofactor binding [GOA01a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0047111 - formate dehydrogenase (cytochrome-c-553) activity [GOA01a]
Cellular Component:
Inferred from experimentGO:0005829 - cytosol [Benoit98]
Inferred from experimentGO:0009326 - formate dehydrogenase complex [Pommier92]
Inferred from experimentGO:0016020 - membrane [Lasserre06]
Inferred by computational analysisGO:0030288 - outer membrane-bounded periplasmic space [DiazMejia09]
Inferred by computational analysisGO:0042597 - periplasmic space [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolismenergy metabolism, carbonanaerobic respiration
metabolismenergy production/transportelectron donors

Unification Links: DIP:DIP-9576N, EcoliWiki:b3894, Mint:MINT-8047511, ModBase:P32176, PR:PRO_000022584, Pride:P32176, Protein Model Portal:P32176, RefSeq:NP_418330, SMR:P32176, Swiss-Model:P32176, UniProt:P32176

Relationship Links: InterPro:IN-FAMILY:IPR006311, InterPro:IN-FAMILY:IPR006443, InterPro:IN-FAMILY:IPR006655, InterPro:IN-FAMILY:IPR006656, InterPro:IN-FAMILY:IPR006657, InterPro:IN-FAMILY:IPR006963, InterPro:IN-FAMILY:IPR009010, InterPro:IN-FAMILY:IPR027467, Pfam:IN-FAMILY:PF00384, Pfam:IN-FAMILY:PF01568, Pfam:IN-FAMILY:PF04879, Prosite:IN-FAMILY:PS00551, Prosite:IN-FAMILY:PS00932, Prosite:IN-FAMILY:PS51318, Prosite:IN-FAMILY:PS51669, Smart:IN-FAMILY:SM00926

Summary:
fdoG encodes the α subunit of formate dehydrogenase O. It has 75% amino acid identity with FdnG - the catalytic, molybdopterin cofactor containing, α subunit of formate dehydrogenase-N. It contains an in-frame TGA (opal) codon that specifies selenocysteine [Plunkett93]

Unlike FdnG, FdoG appears to be located in the cytoplasm [Benoit98] however the use or reporter fusions to determine toplogy of Tat-dependent proteins has been brought into question [Stanley02]


Subunit of formate dehydrogenase: formate dehydrogenase-O, β subunit

Synonyms: FdoH

Gene: fdoH Accession Numbers: EG11857 (MetaCyc), b3893, ECK3886

Locations: inner membrane

Sequence Length: 300 AAs

Molecular Weight: 33.1 kD (from nucleotide sequence)

Molecular Weight: 32.0 kD (experimental) [Pommier92]

pI: 5.4


GO Terms:
Biological Process:
Inferred from experimentGO:0009061 - anaerobic respiration [Pommier92, Abaibou95]
Inferred from experimentGO:0015944 - formate oxidation [Pommier92, Foltz95]
Inferred from experimentGO:0022904 - respiratory electron transport chain [Pommier92]
Inferred from experimentInferred by computational analysisGO:0045333 - cellular respiration [GOA01a, Abaibou95]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a]
Molecular Function:
Inferred from experimentGO:0036397 - formate dehydrogenase (quinone) activity [Pommier92]
Inferred by computational analysisGO:0008863 - formate dehydrogenase (NAD+) activity [GOA01a]
Inferred by computational analysisGO:0009055 - electron carrier activity [Gaudet10]
Inferred by computational analysisGO:0016491 - oxidoreductase activity [Gaudet10]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Inferred by computational analysisGO:0051536 - iron-sulfur cluster binding [UniProtGOA11a]
Inferred by computational analysisGO:0051539 - 4 iron, 4 sulfur cluster binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentGO:0009326 - formate dehydrogenase complex [Pommier92, Abaibou95]
Inferred from experimentInferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, Lasserre06]
Inferred from experimentGO:0031235 - intrinsic component of the cytoplasmic side of the plasma membrane [Benoit98]
Inferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a, GOA01a]

MultiFun Terms: cell structuremembrane
metabolismenergy metabolism, carbonanaerobic respiration
metabolismenergy production/transportelectron donors

Unification Links: EcoliWiki:b3893, ModBase:P0AAJ5, PR:PRO_000022585, Pride:P0AAJ5, Protein Model Portal:P0AAJ5, RefSeq:NP_418329, SMR:P0AAJ5, Swiss-Model:P0AAJ5, UniProt:P0AAJ5

Relationship Links: InterPro:IN-FAMILY:IPR001450, InterPro:IN-FAMILY:IPR006470, InterPro:IN-FAMILY:IPR014603, InterPro:IN-FAMILY:IPR015246, InterPro:IN-FAMILY:IPR017896, InterPro:IN-FAMILY:IPR017900, Pfam:IN-FAMILY:PF09163, Pfam:IN-FAMILY:PF12800, Pfam:IN-FAMILY:PF13247, Prosite:IN-FAMILY:PS00198, Prosite:IN-FAMILY:PS51379

Summary:
fdoH encodes the β subunit of formate dehydrogenase O. It has 100% amino acid identity with FdnH, the [4Fe-4S] containing β subunit of formate dehydrogenase-N.

FdoH is essentially hydrophilic in nature with one predicted α helical region at the C-terminus. The topological orientation of FdoH appears to be the reverse of FdnH, with the bulk of the protein located in the cytoplasm [Benoit98] however the use or reporter fusions to determine toplogy of Tat-dependent proteins has been brought into question [Stanley02].


Subunit of formate dehydrogenase: formate dehydrogenase-O, γ subunit

Synonyms: FdoI

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

Locations: inner membrane

Sequence Length: 211 AAs

Molecular Weight: 24.606 kD (from nucleotide sequence)

pI: 10.3


GO Terms:
Biological Process:
Inferred from experimentGO:0006974 - cellular response to DNA damage stimulus [Khil02]
Inferred from experimentGO:0009061 - anaerobic respiration [Sawers91, Abaibou95]
Inferred from experimentGO:0015944 - formate oxidation [Abaibou95]
Inferred from experimentInferred by computational analysisGO:0045333 - cellular respiration [GOA01a, Abaibou95]
Inferred by computational analysisGO:0022904 - respiratory electron transport chain [GOA01a]
Inferred by computational analysisGO:0055114 - oxidation-reduction process [UniProtGOA11a]
Molecular Function:
Inferred by computational analysisGO:0008863 - formate dehydrogenase (NAD+) activity [GOA01a]
Inferred by computational analysisGO:0020037 - heme binding [Sawers94]
Inferred by computational analysisGO:0036397 - formate dehydrogenase (quinone) activity [Gaudet10]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, DiazMejia09, Daley05]
Inferred from experimentInferred by computational analysisGO:0005887 - integral component of plasma membrane [Benoit98]
Inferred from experimentInferred by computational analysisGO:0009326 - formate dehydrogenase complex [GOA01a, Abaibou95]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a, GOA01a]
Inferred by computational analysisGO:0016021 - integral component of membrane [UniProtGOA11a, Gaudet10, GOA01a]

MultiFun Terms: cell structuremembrane
metabolismbiosynthesis of macromolecules (cellular constituents)large molecule carrierscytochromes
metabolismenergy metabolism, carbonanaerobic respiration
metabolismenergy production/transportelectron donors

Unification Links: EcoliWiki:b3892, ModBase:P0AEL0, PR:PRO_000022586, Protein Model Portal:P0AEL0, RefSeq:NP_418328, SMR:P0AEL0, Swiss-Model:P0AEL0, UniProt:P0AEL0

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

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].


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

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

Chan09: Chan CS, Chang L, Rommens KL, Turner RJ (2009). "Differential Interactions between Tat-specific redox enzyme peptides and their chaperones." J Bacteriol 191(7);2091-101. PMID: 19151138

Chan10: Chan CS, Chang L, Winstone TM, Turner RJ (2010). "Comparing system-specific chaperone interactions with their Tat dependent redox enzyme substrates." FEBS Lett 584(22);4553-8. PMID: 20974141

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

Foltz95: Foltz KR (1995). "Sperm-binding proteins." Int Rev Cytol 163;249-303. PMID: 8522421

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

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

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

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

Stanley02: Stanley NR, Sargent F, Buchanan G, Shi J, Stewart V, Palmer T, Berks BC (2002). "Behaviour of topological marker proteins targeted to the Tat protein transport pathway." Mol Microbiol 43(4);1005-21. PMID: 11929547

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."


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 19.5 on Fri Apr 29, 2016, BIOCYC11A.