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Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
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discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
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Escherichia coli K-12 substr. MG1655 Polypeptide: formate dehydrogenase-O, α subunit



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

Regulation Summary Diagram: ?

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

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].

Gene Citations: [Plunkett93]

Locations: periplasmic space, cytosol, membrane

Map Position: [4,080,795 <- 4,083,845] (87.95 centisomes)
Length: 3051 bp / 1016 aa

Molecular Weight of Polypeptide: 112.55 kD (from nucleotide sequence)

pI: 7.8

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

Unification Links: ASAP:ABE-0012710 , CGSC:33985 , DIP:DIP-9576N , EchoBASE:EB1804 , EcoGene:EG11858 , EcoliWiki:b3894 , Mint:MINT-8047511 , ModBase:P32176 , OU-Microarray:b3894 , PortEco:fdoG , PR:PRO_000022584 , Pride:P32176 , Protein Model Portal:P32176 , RefSeq:NP_418330 , RegulonDB:EG11858 , 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

In Paralogous Gene Group: 222 (14 members)

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 [Pommier92]
GO:0045333 - cellular respiration Inferred from experiment Inferred by computational analysis [GOA01, Sawers91]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01]
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 [GOA01a, GOA01]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, GOA01, Gaudet10]
GO:0030151 - molybdenum ion binding Inferred by computational analysis [GOA01]
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, GOA01]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [GOA01, 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

Essentiality data for fdoG 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]

Subunit of: formate dehydrogenase-O

Synonyms: FDH-O, FDH-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:
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

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:
Last-Curated ? 22-Dec-2010 by Mackie A , Macquarie University


Enzymatic reaction of: formate dehydrogenase-O

EC Number: 1.1.5.6

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

Cofactors or Prosthetic Groups: Mo2+


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 33
[UniProt10]
UniProt: Tat-type signal; Non-Experimental Qualifier: potential;
Conserved-Region 43 -> 106
[UniProt13]
UniProt: 4Fe-4S Mo/W bis-MGD-type.
Metal-Binding-Site 50
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 53
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 57
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 92
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: by similarity;
Selenocysteine-site 196
[UniProt10a]
UniProt: Selenocysteine;
Sequence-Conflict 252 -> 261
[Plunkett93, UniProt10a]
Alternate sequence: GAKLIVIDPR → RREADCDRSC; UniProt: (in Ref. 1; AAB03027);
Sequence-Conflict 344 -> 348
[Plunkett93, UniProt10a]
Alternate sequence: ENGFA → GKRLR; UniProt: (in Ref. 1; AAB03027);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b3894 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11858; 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

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

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

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

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

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

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."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 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
Page generated by SRI International Pathway Tools version 18.5 on Sat Dec 20, 2014, BIOCYC13A.