|Gene:||hybB||Accession Numbers: EG11800 (EcoCyc), b2995, ECK2989|
Component of: hydrogenase 2 (extended summary available)
The HybB protein is predicted to be an integral membrane component of hydrogenase 2 [Menon94]. hybB contains a HXXH conserved motif associated with cytochrome b type proteins [Menon94] HybB contains no conserved hisitidines that would serve as heme iron ligands [Dubini02]. HybB may act as a proton pump during H(2):quinone oxidoreductase activity [Pinske15]
A hybB in-frame deletion mutant can not grow on glycerol and fumarate as the sole energy sources. However, the HybOHybC complex is correctly targeted to the membrane and active with the artificial electron acceptor benzyl viologen (BV) [Dubini02].
Gene Citations: [Sargent98a]
Locations: inner membrane
|Map Position: [3,141,008 <- 3,142,186] (67.7 centisomes, 244°)||Length: 1179 bp / 392 aa|
Molecular Weight of Polypeptide: 43.602 kD (from nucleotide sequence)
Unification Links: ASAP:ABE-0009830, CGSC:33414, EchoBASE:EB1748, EcoGene:EG11800, EcoliWiki:b2995, OU-Microarray:b2995, PortEco:hybB, Protein Model Portal:P37180, RefSeq:NP_417469, RegulonDB:EG11800, String:511145.b2995, UniProt:P37180
In Paralogous Gene Group: 245 (2 members)
|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|
|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]|
Subunit of: hydrogenase 2
Synonyms: HYD2, hydrogenase-2, hydrogen:menaquinone oxidoreductase 2
Subunit composition of
hydrogenase 2 = [HybA][HybB][HybO][HybC]
hydrogenase 2 - [Fe-S] binding, ferredoxin-type component HybA = HybA (summary available)
hydrogenase 2 - integral membrane subunit HybB = HybB (summary available)
hydrogenase 2, small subunit = HybO (summary available)
hydrogenase 2, large subunit = HybC (summary available)
Hydrogenase 2 is a membrane-bound, [Ni-Fe] enzyme produced under anaerobic conditions. Hydrogenase 2 is a respiratory enzyme which couples hydrogen oxidation in the periplasm to reduction of the inner membrane quinone pool [Ballantine86, Sargent98a]. Hydrogenase 2 participates in H(2) dependent reduction of fumarate, dimethyl sulfoxide and trimethylamine N-oxide [Sawers85, Laurinavichene01, Pinske15] (and see [Unden97].
Hydrogenase 2 is an oxygen sensitive enzyme - it is unable to catalyse H(2) oxidation under aerobic conditions [Laurinavichene01, Lukey10]. Hydrogenase 2 functions optimally at redox potentials lower than -100 to -150 mV [Laurinavichene02, Lukey10]. Hydrogenase 2 is capable of bidirectional catalysis in vitro [Lukey10] and in vivo [Pinske15]. Hydrogenase 2 can function as an H(2) evolving enzyme (ie. as a proton reductant) during fermentative growth with glycerol; this endergonic reaction is driven by the membrane proton gradient and probably functions to prevent over reduction of the quinone pool [Pinske15].
Hydrogenase 2 uses menaquinone/demethylmenaquinone to couple hydrogen oxidation to fumarate reduction during anaerobic respiratory growth with glycerol and fumarate and also during H(2) evolution during fermentation with glycerol; hydrogenase 2 can rapidly switch between H(2) evolution and H(2) oxidation modes in vivo [Pinske15].
Trypsin treatment of membranes releases an active, soluble fragment of hydrogenase 2 which consists of the large and small subunits [Ballantine86]. Hydrogenase 2 is encoded within the hyb operon (hybGFEDCBAO); the complete enzyme complex is thought to consist of the HybA, HybB, HybC and HybO subunits [Menon94, Dubini02]. HybOC forms the core catalytic dimer anchored to the membrane via a hydrophobic helix at the C-terminus of HybO; HybA (a ferredoxin type protein) and HybB (an integral membrane protein) are essential for shuttling electrons to the quinone pool [Dubini02, Pinske15].
HybC and HybO are coordinately assembled and processed; acquisition of the [NiFe] cofactor, C-terminal processing of HybC and subsequent association with the small subunit (HybO) are required prior to export by the Tat system [Rodrigue96, Sargent98a, Rodrigue99, Zhang03h, Dubini03]. Maturation and membrane targeting of hydrogenase 2 involves proteins encoded within the hyp and hyb operons ( HypB, HypD, HypE, HybD, HybE and HybG) and the HypF protein (reviews: [Bock06, Forzi07]).
Expression of the hyb operon is induced under anaerobic conditions and repressed by nitrate [Richard99].
E. coli K-12 contains a second membrane associated hydrogenase - hydrogenase 1 - and a third hydrogenase - hydrogenase 3 - which is part of the formate hydrogenlyase complex. A potential fourth hydrogenase - hydrogenase 4 - is encoded within the hyf operon.
Locations: periplasmic space, inner membrane
Enzymatic reaction of: hydrogen:menaquinone oxidoreductase (hydrogenase 2)
EC Number: 184.108.40.206
The representation of the hydrogenase 2 complex depicts the location of the donor (ie. H2) oxidation site and menaquinone reduction site at opposite sides of the membrane (H+/e- = 1). This representation has not been experimentally established.
|Transmembrane-Region||12 -> 32|
|Transmembrane-Region||35 -> 55|
|Transmembrane-Region||59 -> 79|
|Transmembrane-Region||91 -> 111|
|Transmembrane-Region||134 -> 154|
|Transmembrane-Region||169 -> 189|
|Transmembrane-Region||208 -> 228|
|Transmembrane-Region||250 -> 270|
|Transmembrane-Region||282 -> 302|
|Sequence-Conflict||306 -> 307|
|Transmembrane-Region||334 -> 354|
|Transmembrane-Region||356 -> 376|
|Pfam PF03916||45 -> 330|
10/20/97 Gene b2995 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11800; confirmed by SwissProt match.
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
Ballantine86: Ballantine SP, Boxer DH (1986). "Isolation and characterisation of a soluble active fragment of hydrogenase isoenzyme 2 from the membranes of anaerobically grown Escherichia coli." Eur J Biochem 1986;156(2);277-84. PMID: 3516690
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
Dubini02: Dubini A, Pye RL, Jack RL, Palmer T, Sargent F (2002). "How bacteria get energy from hydrogen: a genetic analysis of periplasmic hydrogen oxidationin Escherichia coli." Int J Hydrogen Energy 27(11-12);1413-1420.
Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371
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
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
Laurinavichene01: Laurinavichene TV, Tsygankov AA (2001). "H2 consumption by Escherichia coli coupled via hydrogenase 1 or hydrogenase 2 to different terminal electron acceptors." FEMS Microbiol Lett 202(1);121-4. PMID: 11506918
Laurinavichene02: Laurinavichene TV, Zorin NA, Tsygankov AA (2002). "Effect of redox potential on activity of hydrogenase 1 and hydrogenase 2 in Escherichia coli." Arch Microbiol 178(6);437-42. PMID: 12420163
Lukey10: Lukey MJ, Parkin A, Roessler MM, Murphy BJ, Harmer J, Palmer T, Sargent F, Armstrong FA (2010). "How Escherichia coli is equipped to oxidize hydrogen under different redox conditions." J Biol Chem 285(6);3928-38. PMID: 19917611
Menon94: Menon NK, Chatelus CY, Dervartanian M, Wendt JC, Shanmugam KT, Peck HD, Przybyla AE (1994). "Cloning, sequencing, and mutational analysis of the hyb operon encoding Escherichia coli hydrogenase 2." J Bacteriol 176(14);4416-23. PMID: 8021226
Pinske11: Pinske C, Sawers G (2011). "Iron restriction induces preferential down-regulation of H2-consuming over H2-evolving reactions during fermentative growth of Escherichia coli." BMC Microbiol 11;196. PMID: 21880124
Pinske15: Pinske C, Jaroschinsky M, Linek S, Kelly CL, Sargent F, Sawers RG (2015). "Physiology and bioenergetics of [NiFe]-hydrogenase 2-catalyzed H2-consuming and H2-producing reactions in Escherichia coli." J Bacteriol 197(2);296-306. PMID: 25368299
Richard99: Richard DJ, Sawers G, Sargent F, McWalter L, Boxer DH (1999). "Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli." Microbiology 145 ( Pt 10);2903-12. PMID: 10537212
Rodrigue96: Rodrigue A, Boxer DH, Mandrand-Berthelot MA, Wu LF (1996). "Requirement for nickel of the transmembrane translocation of NiFe-hydrogenase 2 in Escherichia coli." FEBS Lett 392(2);81-6. PMID: 8772179
Rodrigue99: Rodrigue A, Chanal A, Beck K, Muller M, Wu LF (1999). "Co-translocation of a periplasmic enzyme complex by a hitchhiker mechanism through the bacterial tat pathway." J Biol Chem 274(19);13223-8. PMID: 10224080
Sargent98a: Sargent F, Ballantine SP, Rugman PA, Palmer T, Boxer DH (1998). "Reassignment of the gene encoding the Escherichia coli hydrogenase 2 small subunit--identification of a soluble precursor of the small subunit in a hypB mutant." Eur J Biochem 1998;255(3);746-54. PMID: 9738917
Sawers85: 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
Trchounian14: Trchounian A, Gary Sawers R (2014). "Novel insights into the bioenergetics of mixed-acid fermentation: can hydrogen and proton cycles combine to help maintain a proton motive force?." IUBMB Life 66(1);1-7. PMID: 24501007
Unden97: Unden G, Bongaerts J (1997). "Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors." Biochim Biophys Acta 1320(3);217-34. PMID: 9230919
Zhang03h: Zhang M, Pradel N, Mandrand-Berthelot MA, Yu Z, Wu LF (2003). "Effect of alteration of the C-terminal extension on the maturation and folding of the large subunit of the Escherichia coli hydrogenase-2." Biochimie 85(6);575-9. PMID: 12829374
Chung13: Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keles S (2013). "dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data." PLoS Comput Biol 9(10);e1003246. PMID: 24146601
MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305
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