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MetaCyc Transporter: formate dehydrogenase-O

Synonyms: FDH-O, FDH-Z

Species: Escherichia coli K-12 substr. MG1655

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:
The proton motive force (PMF), composed of an electrochemical gradient and a concentration difference of protons across the inner membrane, allows generation of the ubiquitous energy carrier ATP by ATP synthase. The PMF itself can be generated by oxidative phosphorylation, using molecular oxygen as the terminal electron acceptor.

In addition to molecular oxygen, E. coli can use alternative terminal electron acceptors to generate the PMF. Formate dehydrogenase-O is part of one such system. Expression of formate dehydrogenase-O is increased under aerobic conditions; under anaerobic conditions, nitrate stimulates expression slightly [Abaibou95]. The global regulators H-NS and CRP may play a role in regulation of FDH-O expression [Abaibou95]. The physiological role of formate dehydrogenase-O may be the ability to rapidly adapt to anaerobiosis while levels of formate dehydrogenase-N are still insufficient [Abaibou95].

Formate dehydrogenase-O shares extensive sequence similarity and immunological properties with the anaerobically expressed formate dehydrogenase-N [Pommier92, Abaibou95]. FDH-O is a heterotrimeric complex consisting of a an α (FdoG), a β (FdoH) and a γ (FdoI) subunit. FDH-O is a molybdo-selenoprotein and has four cysteine clusters involved in the foration of iron-sulfur centres [Sawers94].

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].

Locations: inner membrane

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Pommier92]
GO:0022904 - respiratory electron transport chain Inferred from experiment [Pommier92]
GO:0045333 - cellular respiration Inferred from experiment [Sawers91]
Molecular Function: GO:0008863 - formate dehydrogenase (NAD+) activity Inferred from experiment [Pommier92]
GO:0009055 - electron carrier activity Inferred from experiment [Pommier92]
Cellular Component: GO:0009326 - formate dehydrogenase complex Inferred from experiment [Pommier92]
GO:0005886 - plasma membrane [Pommier92]

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: formate dehydrogenase-O

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

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Cofactors or Prosthetic Groups: Mo2+


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

Synonyms: FdoG

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

Locations: periplasmic space, cytosol, membrane

Sequence Length: 1016 AAs

Molecular Weight: 112.55 kD (from nucleotide sequence)

pI: 7.8

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0009061 - anaerobic respiration Inferred from experiment [Pommier92]
GO:0045333 - cellular respiration Inferred from experiment Inferred by computational analysis [GOA01a, Sawers91]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Chan10, Chan09, Arifuzzaman06]
GO:0043546 - molybdopterin cofactor binding Inferred by computational analysis Inferred from experiment [Pommier92, Sawers94]
GO:0008863 - formate dehydrogenase (NAD+) activity Inferred by computational analysis [GOA01, GOA01a]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01a, Gaudet10]
GO:0030151 - molybdenum ion binding Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [GOA01a, Benoit98]
GO:0009326 - formate dehydrogenase complex Inferred from experiment [Pommier92]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005829 - cytosol [Benoit98]
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron 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 , String:511145.b3894 , 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:PS00490 , Prosite:IN-FAMILY:PS00551 , Prosite:IN-FAMILY:PS00932 , Prosite:IN-FAMILY:PS51318 , Prosite:IN-FAMILY:PS51669 , Smart:IN-FAMILY:SM00926

Summary:
By similarity to the paralogous α subunit of formate dehydrogenase-N, FdnG, FdoG is thought to be the catalytic subunit of formate dehydrogenase-O, containing the bis-molybdopterin guanine dinucleotide (MGD) cofactor and selenocysteine [Sawers91].

Unlike FdnG, FdoG appears to be located in the cytoplasm [Benoit98].


Subunit of formate dehydrogenase-O: 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)

pI: 5.4

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Pommier92]
GO:0045333 - cellular respiration Inferred from experiment Inferred by computational analysis [GOA01a, Sawers91]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008863 - formate dehydrogenase (NAD+) activity Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, Sawers94]
Cellular Component: GO:0005887 - integral component of plasma membrane Inferred from experiment [Benoit98]
GO:0009326 - formate dehydrogenase complex Inferred from experiment [Pommier92]
GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Lasserre06]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, DiazMejia09]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: cell structure membrane
metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron donors

Unification Links: EcoliWiki:b3893 , ModBase:P0AAJ5 , PR:PRO_000022585 , Pride:P0AAJ5 , Protein Model Portal:P0AAJ5 , RefSeq:NP_418329 , SMR:P0AAJ5 , String:511145.b3893 , 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:
By similarity to the paralogous β subunit of formate dehydrogenase-N, FdnH, FdoH is thought to contain four [4Fe-4S] clusters and one C-terminal transmembrane helix [Sawers91, Benoit98]. The topological orientation of FdoH appears to be the reverse of the orientation of FdnH, with the [4Fe-4S] cluster-containing N-terminus located in the cytoplasm [Benoit98].

By analogy with FdnH, FdoH may serve as a conduit for electrons that are proposed to be transferred from the formate oxidation site in FdoG to the menaquinone associated with the FdoI subunit of formate dehydrogenase-O.


Subunit of formate dehydrogenase-O: 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: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Khil02]
GO:0009061 - anaerobic respiration Inferred from experiment [Pommier92]
GO:0045333 - cellular respiration Inferred from experiment Inferred by computational analysis [GOA01a, Sawers91]
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 [Benoit98]
GO:0009326 - formate dehydrogenase complex Inferred from experiment Inferred by computational analysis [GOA01a, Pommier92]
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

Unification Links: EcoliWiki:b3892 , ModBase:P0AEL0 , PR:PRO_000022586 , Protein Model Portal:P0AEL0 , RefSeq:NP_418328 , SMR:P0AEL0 , String:511145.b3892 , Swiss-Model:P0AEL0 , UniProt:P0AEL0

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

Summary:
By similarity to the paralogous γ subunit of formate dehydrogenase-N, FdnI, FdoI is the heme-containing membrane subunit of formate dehydrogenase-O.

Both the N- and C-terminus of FdoI appear to be located in the cytoplasm [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

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

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

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 18.5 on Fri Nov 28, 2014, biocyc12.