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Escherichia coli K-12 substr. MG1655 Polypeptide: hydrogenase 3 and formate hydrogenlyase complex, HycG subunit



Gene: hycG Accession Numbers: EG10480 (EcoCyc), b2719, ECK2714

Synonyms: hevG

Regulation Summary Diagram: ?

Regulation summary diagram for hycG

Component of:
hydrogenase 3 (extended summary available)
formate hydrogenlyase complex

Summary:
The hycBCDEFG genes in E.coli K-12 encode the hydrogenase component (hydrogenase 3) of the formate hydrogenlyase complex. HycG has similarity to small subunits of hydrogenases [Sauter et al., 1992] and resembles one of the subunits of NADH:ubiquinone oxidoreductase of the respiratory chain [Bohm et al., 1990, Sawers et al., 2004].

Gene Citations: [Hopper94, Rossmann et al., 1995]

Locations: cytosol

Map Position: [2,841,465 <- 2,842,232] (61.24 centisomes, 220°)
Length: 768 bp / 255 aa

Molecular Weight of Polypeptide: 27.999 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0008936 , CGSC:33151 , DIP:DIP-9977N , EchoBASE:EB0475 , EcoGene:EG10480 , EcoliWiki:b2719 , Mint:MINT-1287919 , ModBase:P16433 , OU-Microarray:b2719 , PortEco:hycG , PR:PRO_000022959 , Protein Model Portal:P16433 , RefSeq:NP_417199 , RegulonDB:EG10480 , SMR:P16433 , String:511145.b2719 , Swiss-Model:P16433 , UniProt:P16433

Relationship Links: InterPro:IN-FAMILY:IPR006137 , InterPro:IN-FAMILY:IPR006138 , Panther:IN-FAMILY:PTHR11995 , Pfam:IN-FAMILY:PF01058 , Prosite:IN-FAMILY:PS01150

In Paralogous Gene Group: 404 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for hycG

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Rajagopala et al., 2012, Butland05]
GO:0008137 - NADH dehydrogenase (ubiquinone) activity Inferred by computational analysis [GOA01a]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0048038 - quinone binding Inferred by computational analysis [GOA01a]
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, GOA01a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0009375 - ferredoxin hydrogenase complex Inferred by computational analysis [Bohm et al., 1990]

MultiFun Terms: metabolism energy metabolism, carbon fermentation

Essentiality data for hycG 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: hydrogenase 3

Subunit composition of hydrogenase 3 = [HycD][HycC][HycF][HycG][HycB][HycE]
         hydrogenase 3, membrane subunit = HycD (summary available)
         hydrogenase 3, membrane subunit = HycC (summary available)
         formate hydrogenlyase complex iron-sulfur protein = HycF (summary available)
         hydrogenase 3 and formate hydrogenlyase complex, HycG subunit = HycG (summary available)
         hydrogenase 3, Fe-S subunit = HycB (summary available)
         hydrogenase 3, large subunit = HycE (extended summary available)

Component of: formate hydrogenlyase complex

Summary:
Microbial hydrogenases catalyse the reversible reduction of protons to molecular hydrogen. E. coli hydrogenase 3, encoded by the hyc genes (hycD, hycC, hycF, hycG, hycB and hycE), is a multisubunit enzyme that forms part of the formate hydrogenlyase (FHL) complex responsible for the fermentative or anaerobic oxidation of formic acid to carbon dioxide and molecular hydrogen [Peck & Gest, 1957, Sawers et al., 1985, Bohm et al., 1990, Bagramyan & Trchounian, 2003].

Hydrogenase 3 functions primarily in the production of H2 [Maeda et al., 2007] and is important for H2 production at acidic pH [Bagramyan et al., 2002, Mnatsakanyan et al., 2004, Noguchi et al., 2010]. Hydrogen uptake in a strain lacking hydrogenase 1 and hydrogenase 2 is further reduced by the incorporation of a hycE mutation, suggesting that hydrogenase 3 can also function in hydrogen uptake [Maeda et al., 2007]. Hydrogenase 3 shows a high tolerance to product (H2) inhibition [McDowall et al., 2014].

Hydrogenase 3 is a membrane associated H2 evolving respiratory [NiFe] hydrogenase. It contains the large (HycE) and small (HycG) subunits that are characteristic of 'standard' NiFe hydrogenases plus two additional hydrophilic subunits (HycB and HycF) and two inner membrane subunits (HycC and HycD). Fe-S prosthetic groups located in the hydrophilic part of the complex may form the electron transport pathway (reviews: [Vignais et al., 2001, Hedderich & Forzi, 2005, Vignais, 2008]). Isolation of FHL using affinity chromatography indicates the presence of a core complex containing HycE, HycB HycF HycG and FdhF which has formate hydrogenlyase activity in vitro; a larger complex containing the membrane assoicated subunits HyC and HycD is isolated in the presence of detergent [McDowall et al., 2014]

Formate oxidation in an anaerobically grown fermenting E. coli strain lacking hydrogenase 1 and hydrogenase 2 enzymes generates membrane potential [Hakobyan et al., 2005].

Sequence similarity between the genes encoding hydrogenase 3 and those encoding subunits that form the core of energy conserving NADH:quinone oxidoreductase (complex I) has been reported [Bohm et al., 1990] and an evolutionary relationship between the two has been proposed [Hedderich, 2004].

Strains with insertion mutations of genes within the hyc operon are defective for hydrogenase activity [Pecher et al., 1983, Yerkes et al., 1984].

Hydrogenase 3 is a nickel containing Fe-S protein [Rossmann et al., 1994].

The hyc operon is regulated coordinately with the structural gene for formate dehydrogenase H. Expression is repressed by oxygen and by nitrate and induced by formate under fermentative growth conditions [Pecher et al., 1983, Yerkes et al., 1984]. Formate is an obligate inducer of the formate hydrogenlyase complex genes [Birkmann et al., 1987].

E. coli K-12 contains three other hydrogenases: hydrogenase 1 and hydrogenase 2 (respiratory enzymes that function in H2 uptake) and hydrogenase 4 (less well characterised; possibly silent).

Reviews: [Sawers, 1994, Lin & Iuchi, 1991, Trchounian et al., 2012]

Locations: inner membrane

GO Terms:

Biological Process: GO:0006113 - fermentation Inferred from experiment [Peck & Gest, 1957]
GO:0015990 - electron transport coupled proton transport Inferred by computational analysis Inferred from experiment [Hakobyan et al., 2005, Vignais, 2008]
Molecular Function: GO:0008901 - ferredoxin hydrogenase activity Inferred from experiment [McDowall et al., 2014]
GO:0033748 - hydrogenase (acceptor) activity Inferred from experiment [Bohm et al., 1990, Pecher et al., 1983]
Cellular Component: GO:0009375 - ferredoxin hydrogenase complex Inferred by computational analysis Inferred from experiment [McDowall et al., 2014, Bohm et al., 1990]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Bohm et al., 1990]

Credits:
Last-Curated ? 14-Sep-2014 by Mackie A , Macquarie University


Enzymatic reaction of: hydrogenase

a reduced hydrogenase 3 + H+ <=> an oxidized hydrogenase 3 + H2

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

This reaction is reversible.


Subunit of: formate hydrogenlyase complex

Subunit composition of formate hydrogenlyase complex = [FdhF][(HycD)(HycC)(HycF)(HycG)(HycB)(HycE)]
         formate dehydrogenase H = FdhF (extended summary available)
         hydrogenase 3 = (HycD)(HycC)(HycF)(HycG)(HycB)(HycE) (extended summary available)
                 hydrogenase 3, membrane subunit = HycD (summary available)
                 hydrogenase 3, membrane subunit = HycC (summary available)
                 formate hydrogenlyase complex iron-sulfur protein = HycF (summary available)
                 hydrogenase 3 and formate hydrogenlyase complex, HycG subunit = HycG (summary available)
                 hydrogenase 3, Fe-S subunit = HycB (summary available)
                 hydrogenase 3, large subunit = HycE (extended summary available)


Enzymatic reaction of: formate hydrogenlyase complex

Synonyms: FHL-complex

formate + H+ <=> CO2 + H2

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

In Pathways: mixed acid fermentation


Sequence Features

Protein sequence of hydrogenase 3 and formate hydrogenlyase complex, HycG subunit with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 45
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 51
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;
Sequence-Conflict 57
[Bohm et al., 1990, UniProt10a]
UniProt: (in Ref. 1; CAA35552);
Metal-Binding-Site 115
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;
Metal-Binding-Site 145
[UniProt10]
UniProt: Iron-sulfur (4Fe-4S); Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Notes:

History:
10/20/97 Gene b2719 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10480; 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

Bagramyan & Trchounian, 2003: Bagramyan K, Trchounian A (2003). "Structural and functional features of formate hydrogen lyase, an enzyme of mixed-acid fermentation from Escherichia coli." Biochemistry (Mosc) 68(11);1159-70. PMID: 14640957

Bagramyan et al., 2002: Bagramyan K, Mnatsakanyan N, Poladian A, Vassilian A, Trchounian A (2002). "The roles of hydrogenases 3 and 4, and the F0F1-ATPase, in H2 production by Escherichia coli at alkaline and acidic pH." FEBS Lett 516(1-3);172-8. PMID: 11959127

Birkmann et al., 1987: Birkmann A, Zinoni F, Sawers G, Bock A (1987). "Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli." Arch Microbiol 1987;148(1);44-51. PMID: 2443100

Bohm et al., 1990: Bohm R, Sauter M, Bock A (1990). "Nucleotide sequence and expression of an operon in Escherichia coli coding for formate hydrogenlyase components." Mol Microbiol 1990;4(2);231-43. PMID: 2187144

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

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."

Hakobyan et al., 2005: Hakobyan M, Sargsyan H, Bagramyan K (2005). "Proton translocation coupled to formate oxidation in anaerobically grown fermenting Escherichia coli." Biophys Chem 115(1);55-61. PMID: 15848284

Hedderich & Forzi, 2005: Hedderich R, Forzi L (2005). "Energy-converting [NiFe] hydrogenases: more than just H2 activation." J Mol Microbiol Biotechnol 10(2-4);92-104. PMID: 16645307

Hedderich, 2004: Hedderich R (2004). "Energy-converting [NiFe] hydrogenases from archaea and extremophiles: ancestors of complex I." J Bioenerg Biomembr 36(1);65-75. PMID: 15168611

Hopper94: Hopper S, Babst M, Schlensog V, Fischer HM, Hennecke H, Bock A (1994). "Regulated expression in vitro of genes coding for formate hydrogenlyase components of Escherichia coli." J Biol Chem 1994;269(30);19597-604. PMID: 8034728

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

Lin & Iuchi, 1991: Lin EC, Iuchi S (1991). "Regulation of gene expression in fermentative and respiratory systems in Escherichia coli and related bacteria." Annu Rev Genet 1991;25;361-87. PMID: 1812811

Maeda et al., 2007: Maeda T, Sanchez-Torres V, Wood TK (2007). "Escherichia coli hydrogenase 3 is a reversible enzyme possessing hydrogen uptake and synthesis activities." Appl Microbiol Biotechnol 76(5);1035-42. PMID: 17668201

McDowall et al., 2014: McDowall JS, Murphy BJ, Haumann M, Palmer T, Armstrong FA, Sargent F (2014). "Bacterial formate hydrogenlyase complex." Proc Natl Acad Sci U S A 111(38);E3948-56. PMID: 25157147

Mnatsakanyan et al., 2004: Mnatsakanyan N, Bagramyan K, Trchounian A (2004). "Hydrogenase 3 but not hydrogenase 4 is major in hydrogen gas production by Escherichia coli formate hydrogenlyase at acidic pH and in the presence of external formate." Cell Biochem Biophys 41(3);357-66. PMID: 15509886

Noguchi et al., 2010: Noguchi K, Riggins DP, Eldahan KC, Kitko RD, Slonczewski JL (2010). "Hydrogenase-3 contributes to anaerobic acid resistance of Escherichia coli." PLoS One 5(4);e10132. PMID: 20405029

Pecher et al., 1983: Pecher A, Zinoni F, Jatisatienr C, Wirth R, Hennecke H, Bock A (1983). "On the redox control of synthesis of anaerobically induced enzymes in enterobacteriaceae." Arch Microbiol 136(2);131-6. PMID: 6360066

Peck & Gest, 1957: Peck HD, Gest H (1957). "Formic dehydrogenase and the hydrogenlyase enzyme complex in coli-aerogenes bacteria." J Bacteriol 73(6);706-21. PMID: 13449036

Rajagopala et al., 2012: Rajagopala SV, Sikorski P, Caufield JH, Tovchigrechko A, Uetz P (2012). "Studying protein complexes by the yeast two-hybrid system." Methods 58(4);392-9. PMID: 22841565

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

Rossmann et al., 1994: Rossmann R, Sauter M, Lottspeich F, Bock A (1994). "Maturation of the large subunit (HYCE) of Escherichia coli hydrogenase 3 requires nickel incorporation followed by C-terminal processing at Arg537." Eur J Biochem 220(2);377-84. PMID: 8125094

Rossmann et al., 1995: Rossmann R, Maier T, Lottspeich F, Bock A (1995). "Characterisation of a protease from Escherichia coli involved in hydrogenase maturation." Eur J Biochem 227(1-2);545-50. PMID: 7851435

Sauter et al., 1992: Sauter M, Bohm R, Bock A (1992). "Mutational analysis of the operon (hyc) determining hydrogenase 3 formation in Escherichia coli." Mol Microbiol 1992;6(11);1523-32. PMID: 1625581

Sawers et al., 1985: Sawers RG, Ballantine SP, Boxer DH (1985). "Differential expression of hydrogenase isoenzymes in Escherichia coli K-12: evidence for a third isoenzyme." J Bacteriol 164(3);1324-31. PMID: 3905769

Sawers et al., 2004: Sawers RG, Blokesch M, Boeck A (2004). "Anaerobic Formate and Hydrogen Metabolism." Escherichia coli and Salmonella, Cellular and Molecular Biology.

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

Trchounian et al., 2012: Trchounian K, Poladyan A, Vassilian A, Trchounian A (2012). "Multiple and reversible hydrogenases for hydrogen production by Escherichia coli: dependence on fermentation substrate, pH and the F(0)F(1)-ATPase." Crit Rev Biochem Mol Biol 47(3);236-49. PMID: 22313414

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.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Vignais et al., 2001: Vignais PM, Billoud B, Meyer J (2001). "Classification and phylogeny of hydrogenases." FEMS Microbiol Rev 25(4);455-501. PMID: 11524134

Vignais, 2008: Vignais PM (2008). "Hydrogenases and H(+)-reduction in primary energy conservation." Results Probl Cell Differ 45;223-52. PMID: 18500479

Yerkes et al., 1984: Yerkes JH, Casson LP, Honkanen AK, Walker GC (1984). "Anaerobiosis induces expression of ant, a new Escherichia coli locus with a role in anaerobic electron transport." J Bacteriol 158(1);180-6. PMID: 6425260

Other References Related to Gene Regulation

Hasona98: Hasona A, Self WT, Ray RM, Shanmugam KT (1998). "Molybdate-dependent transcription of hyc and nar operons of Escherichia coli requires MoeA protein and ModE-molybdate." FEMS Microbiol Lett 169(1);111-6. PMID: 9851041

Hasona98a: Hasona A, Ray RM, Shanmugam KT (1998). "Physiological and genetic analyses leading to identification of a biochemical role for the moeA (molybdate metabolism) gene product in Escherichia coli." J Bacteriol 180(6);1466-72. PMID: 9515915

Leonhartsberger00: Leonhartsberger S, Ehrenreich A, Bock A (2000). "Analysis of the domain structure and the DNA binding site of the transcriptional activator FhlA." Eur J Biochem 267(12);3672-84. PMID: 10848985

Leonhartsberger01: Leonhartsberger S, Huber A, Lottspeich F, Bock A (2001). "The hydH/G Genes from Escherichia coli code for a zinc and lead responsive two-component regulatory system." J Mol Biol 2001;307(1);93-105. PMID: 11243806

Lutz90: Lutz S, Bohm R, Beier A, Bock A (1990). "Characterization of divergent NtrA-dependent promoters in the anaerobically expressed gene cluster coding for hydrogenase 3 components of Escherichia coli." Mol Microbiol 1990;4(1);13-20. PMID: 2181234

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291

Schlensog94: Schlensog V, Lutz S, Bock A (1994). "Purification and DNA-binding properties of FHLA, the transcriptional activator of the formate hydrogenlyase system from Escherichia coli." J Biol Chem 1994;269(30);19590-6. PMID: 8034727

Self00: Self WT, Shanmugam KT (2000). "Isolation and characterization of mutated Fh1A proteins which activate transcription of the hyc operon (formate hydrogenlyase) of Escherichia coli in the absence of molybdate(1)." FEMS Microbiol Lett 184(1);47-52. PMID: 10689164

Self99: Self WT, Grunden AM, Hasona A, Shanmugam KT (1999). "Transcriptional regulation of molybdoenzyme synthesis in Escherichia coli in response to molybdenum: ModE-molybdate, a repressor of the modABCD (molybdate transport) operon is a secondary transcriptional activator for the hyc and nar operons." Microbiology 1999;145 ( Pt 1);41-55. PMID: 10206709


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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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