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MetaCyc Transporter: hydrogenase 2

Synonyms: HYD2, hydrogenase-2, hydrogen:menaquinone oxidoreductase 2

Species: Escherichia coli K-12 substr. MG1655

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)

Summary:
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, Pinske14] (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 [Pinske14]. 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 [Pinske14].

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 [Pinske14].

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, Pinske14].

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, Zhang03l, 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.

Reviews: [Sawers94, Vignais04]

Citations: [Pinske11, Ballantine85]

Locations: periplasmic space, inner membrane

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Pinske14, Menon94, Sawers85]
GO:0019588 - anaerobic glycerol catabolic process Inferred from experiment [Pinske14]
GO:0019645 - anaerobic electron transport chain Inferred from experiment [Laurinavichene01, Pinske14]
GO:1902421 - hydrogen metabolic process Inferred from experiment [Sawers85]
Molecular Function: GO:0005506 - iron ion binding Inferred from experiment [Ballantine86]
GO:0009055 - electron carrier activity Inferred from experiment [Laurinavichene01]
GO:0016151 - nickel cation binding Inferred from experiment [Ballantine86]
GO:0033748 - hydrogenase (acceptor) activity Inferred from experiment [Laurinavichene02, Sargent98a, Ballantine86]
GO:0047067 - hydrogen:quinone oxidoreductase activity Inferred from experiment [Pinske14]
Cellular Component: GO:0031236 - extrinsic component of periplasmic side of plasma membrane Inferred from experiment [Rodrigue99]
GO:0044569 - [Ni-Fe] hydrogenase complex Inferred by computational analysis Inferred from experiment [Dubini02, Menon94, Ballantine86]

Credits:
Revised in EcoCyc 12-Jan-2015 by Mackie A , Macquarie University
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International


Enzymatic reaction of: hydrogen:menaquinone oxidoreductase (hydrogenase 2)

Transport reaction diagram for hydrogen:menaquinone oxidoreductase

Alternative Substrates for a menaquinone: benzyl viologen [Ballantine86 ]

In Pathways: hydrogen to fumarate electron transfer , hydrogen to dimethyl sulfoxide electron transfer , hydrogen to trimethylamine N-oxide electron transfer

Credits:
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International

Summary:
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.

Cofactors or Prosthetic Groups: a nickel-iron-sulfur cluster [Ballantine86], a [FeS] iron-sulfur cluster [Sargent98a]

Inhibitors (Unknown Mechanism): Cu2+ [Ballantine86] , N-bromosuccinimide [Ballantine86] , Co2+ [Ballantine86]


Subunit of hydrogenase 2: hydrogenase 2 - [Fe-S] binding, ferredoxin-type component HybA

Synonyms: HydL, HybA

Gene: hybA Accession Numbers: EG11799 (MetaCyc), b2996, ECK2990

Locations: periplasmic space, cytosol, inner membrane

Sequence Length: 328 AAs

Molecular Weight: 36.003 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Dubini02, Menon94]
GO:0019588 - anaerobic glycerol catabolic process Inferred from experiment [Pinske14]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0033748 - hydrogenase (acceptor) activity Inferred from experiment [Dubini02]
GO:0047067 - hydrogen:quinone oxidoreductase activity Inferred from experiment [Pinske14]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a, Gaudet10]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a, Menon94]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0044569 - [Ni-Fe] hydrogenase complex Inferred from experiment [Dubini02]
GO:0005737 - cytoplasm Inferred by computational analysis [Gaudet10]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Hatzixanthis03]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolism energy production/transport electron donors

Unification Links: EcoliWiki:b2996 , ModBase:P0AAJ8 , PR:PRO_000022948 , Protein Model Portal:P0AAJ8 , RefSeq:NP_417470 , SMR:P0AAJ8 , String:511145.b2996 , UniProt:P0AAJ8

Relationship Links: InterPro:IN-FAMILY:IPR001450 , InterPro:IN-FAMILY:IPR017896 , InterPro:IN-FAMILY:IPR017900 , InterPro:IN-FAMILY:IPR019546 , Pfam:IN-FAMILY:PF00037 , Pfam:IN-FAMILY:PF12798 , Pfam:IN-FAMILY:PF12838 , Prosite:IN-FAMILY:PS00198 , Prosite:IN-FAMILY:PS51379

Summary:
The hybA-encoded protein may be involved in the periplasmic electron-transferring activity of hydrogenase 2 during catalytic turnover [Sargent98a]. hybA contains a single C-terminal transmembrane helix; HybA is assembled in a Tat-dependent manner [Hatzixanthis03]. hybA contains 16 cysteines and contains 4 predicted [Fe-S] binding sites [Menon94]

An hybA in-frame deletion mutant can not grow on glycerol and fumarate as the sole energy sources, and its reduced fumarate-dependent hydrogen uptake activity is comparable to a hybC deletion mutant; however, the HybOHybC complex is correctly targeted to the membrane [Dubini02]. HybA is essential for electron transfer from H(2) to the quinone pool; it is also essential for the H(2) evolving redox reaction; it is not required for electron transfer to and from redox active viologen dyes in whole cells of E. coli [Pinske14].


Subunit of hydrogenase 2: hydrogenase 2 - integral membrane subunit HybB

Synonyms: HybB

Gene: hybB Accession Numbers: EG11800 (MetaCyc), b2995, ECK2989

Locations: inner membrane

Sequence Length: 392 AAs

Molecular Weight: 43.602 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Menon94, Dubini02]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0033748 - hydrogenase (acceptor) activity Inferred from experiment [Dubini02]
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:0044569 - [Ni-Fe] hydrogenase complex Inferred from experiment [Dubini02]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis [Menon94]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a]

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:b2995 , Protein Model Portal:P37180 , RefSeq:NP_417469 , String:511145.b2995 , UniProt:P37180

Relationship Links: InterPro:IN-FAMILY:IPR005614 , Pfam:IN-FAMILY:PF03916

Summary:
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 [Pinske14]

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].


Subunit of hydrogenase 2: hydrogenase 2, small subunit

Synonyms: YghV, HybO, hydrogenase 2 β subunit

Gene: hybO Accession Numbers: G7554 (MetaCyc), b2997, ECK2991

Locations: inner membrane, periplasmic space

Sequence Length: 372 AAs

Molecular Weight: 39.652 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Menon94]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Chan10, Chan09, Butland06, Butland05]
GO:0008901 - ferredoxin hydrogenase activity Inferred by computational analysis [GOA01a]
GO:0009055 - electron carrier activity Inferred by computational analysis
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0033748 - hydrogenase (acceptor) activity 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, GOA01a, Sargent98a]
GO:0051538 - 3 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Lasserre06]
GO:0031236 - extrinsic component of periplasmic side of plasma membrane Inferred from experiment [Sargent98a, Rodrigue99]
GO:0044569 - [Ni-Fe] hydrogenase complex Inferred from experiment [Dubini02]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, Rodrigue96]
GO:0009375 - ferredoxin hydrogenase complex Inferred by computational analysis [GOA01a]
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-36024N , EcoliWiki:b2997 , Mint:MINT-8046452 , ModBase:P69741 , PR:PRO_000022953 , Protein Model Portal:P69741 , RefSeq:NP_417471 , SMR:P69741 , String:511145.b2997 , Swiss-Model:P69741 , UniProt:P69741

Relationship Links: InterPro:IN-FAMILY:IPR001821 , InterPro:IN-FAMILY:IPR006137 , InterPro:IN-FAMILY:IPR006311 , InterPro:IN-FAMILY:IPR019546 , InterPro:IN-FAMILY:IPR027394 , Panther:IN-FAMILY:PTHR30013 , Pfam:IN-FAMILY:PF01058 , Pfam:IN-FAMILY:PF14720 , Prints:IN-FAMILY:PR00614 , Prosite:IN-FAMILY:PS51318

Summary:
HybO is the small subunit of hydrogenase 2; sequence analysis suggests it contains three Fe-S clusters; expected to be two [4Fe-4S] and one [3Fe-4S] as has been shown by x-ray crystallography for the small subunit of a Desulfovibrio gigas [Ni-Fe] hydrogenase [Sargent98a, Volbeda95]. HybO contains a twin-arginine signal sequence which is required for membrane targeting by the Tat system. HybO accumulates in a soluble precursor form in a hypB mutant which is unable to insert nickel into the large subunit (HybC) of hydrogenase 2 [Sargent98a].

HybO and HybC are coordinately assembled and processed; the presence of both subunits, acquisition of the [Ni-Fe] cofactor and subsequent processing of HybC are required for export of the complex by the Tat system [Rodrigue96, Rodrigue99].

Review: [Vignais04]


Subunit of hydrogenase 2: hydrogenase 2, large subunit

Synonyms: HybC, hydrogenase 2, α subunit

Gene: hybC Accession Numbers: EG11801 (MetaCyc), b2994, ECK2988

Locations: inner membrane

Sequence Length: 567 AAs

Molecular Weight: 62.491 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred from experiment [Dubini02]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0033748 - hydrogenase (acceptor) activity Inferred from experiment Inferred by computational analysis [GOA01, Dubini02]
GO:0005506 - iron ion binding Inferred by computational analysis [Dubini02]
GO:0008901 - ferredoxin hydrogenase activity Inferred by computational analysis [GOA01a]
GO:0016151 - nickel cation binding Inferred by computational analysis [GOA01a, Menon94]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0031236 - extrinsic component of periplasmic side of plasma membrane Inferred from experiment [Sargent98a, Rodrigue99]
GO:0044569 - [Ni-Fe] hydrogenase complex Inferred from experiment [Dubini02]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]

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

Unification Links: DIP:DIP-36022N , EcoliWiki:b2994 , Mint:MINT-1254866 , PR:PRO_000022949 , Pride:P0ACE0 , Protein Model Portal:P0ACE0 , RefSeq:NP_417468 , SMR:P0ACE0 , String:511145.b2994 , UniProt:P0ACE0

Relationship Links: InterPro:IN-FAMILY:IPR001501 , InterPro:IN-FAMILY:IPR018194 , InterPro:IN-FAMILY:IPR029014 , Pfam:IN-FAMILY:PF00374 , Prosite:IN-FAMILY:PS00507 , Prosite:IN-FAMILY:PS00508

Summary:
HybC is the large, [NiFe] containing subunit of hydrogenase 2. The nickel and iron atoms are coordinated by 4 Cys thiolates plus 3 diatomic ligands (2 cyano and a carbonyl). 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, Rodrigue99, Zhang03l, Dubini03] (and reviewed in [Forzi07].


References

Ballantine85: Ballantine SP, Boxer DH (1985). "Nickel-containing hydrogenase isoenzymes from anaerobically grown Escherichia coli K-12." J Bacteriol 163(2);454-9. PMID: 3894325

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

Bock06: Bock A, King PW, Blokesch M, Posewitz MC (2006). "Maturation of hydrogenases." Adv Microb Physiol 51;1-71. PMID: 17091562

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

Butland06: Butland G, Zhang JW, Yang W, Sheung A, Wong P, Greenblatt JF, Emili A, Zamble DB (2006). "Interactions of the Escherichia coli hydrogenase biosynthetic proteins: HybG complex formation." FEBS Lett 580(2);677-81. PMID: 16412426

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

Dubini02: Dubini A, Pye RL, Jack RL, Palmer T, Sargent F (2002). "How bacteria get energy from hydrogen: a genetic analysis of periplasmic hydrogen oxidation in Escherichia coli." Int J Hydrogen Energy 27(11-12);1413-1420.

Dubini03: Dubini A, Sargent F (2003). "Assembly of Tat-dependent [NiFe] hydrogenases: identification of precursor-binding accessory proteins." FEBS Lett 549(1-3);141-6. PMID: 12914940

Forzi07: Forzi L, Sawers RG (2007). "Maturation of [NiFe]-hydrogenases in Escherichia coli." Biometals 20(3-4);565-78. PMID: 17216401

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."

Hatzixanthis03: Hatzixanthis K, Palmer T, Sargent F (2003). "A subset of bacterial inner membrane proteins integrated by the twin-arginine translocase." Mol Microbiol 49(5);1377-90. PMID: 12940994

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

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

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Pinske14: 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

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Zhang03l: 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


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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 19.0 on Tue Sep 1, 2015, biocyc11.