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Escherichia coli K-12 substr. MG1655 Transporter: hydrogenase 2

Synonyms: HYD2, hydrogenase-2

Subunit composition of hydrogenase 2 = [HybA][HybB][HybO][HybC]
         hydrogenase 2 4Fe-4S ferredoxin-type component = HybA (summary available)
         predicted hydrogenase 2 cytochrome b type component = HybB (summary available)
         hydrogenase 2, small subunit = HybO (summary available)
         hydrogenase 2, large subunit = HybC (summary available)

Summary:
There are four hydrogenases in E. coli which are synthesized in response to different physiological conditions. Hydrogenase 2 is a membrane-bound, nickel containing enzyme produced under anaerobic conditions. It is thought that hydrogenase 2 catalyzes the H2-dependent reduction of quinone [Ballantine86, Sawers94, Sargent98a].

Trypsin treatment of membranes releases an active, soluble fragment of hydrogenase 2 which consists of the large and small subunits [Ballantine86]. The complete enzyme complex is thought to consist of the HybA, HybB, HybC, and HybO subunits [Dubini02].

The substrate specificity of hydrogenase 2 for various quinones is unknown [Laurinavichene01].

Hydrogenase 2 activity is reduced in a feoB null strain and eliminated in a feoB/entC double null mutant indicating that the principal route of iron uptake for the synthesis of this enzyme is via the ferrous iron and ferric enterobactin systems [Pinske11].

Locations: periplasmic space

Gene-Reaction Schematic: ?

GO Terms:

Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space [Rodrigue99]


Enzymatic reaction of: hydrogenase

EC Number: 1.12.99.6

Summary:
The representation of the hydrogenase 2 complex indiates transfer of protons across the membrane where protons from MQH2 (or QH2) are produced at the periplasmic side of the complex. This representation has not been experimentally established and is therefore speculative.

Cofactors or Prosthetic Groups: Fe2+ [Comment 1], Ni2+ [Comment 2]

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


Subunit of hydrogenase 2: hydrogenase 2 4Fe-4S ferredoxin-type component

Synonyms: HydL, HybA

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

Locations: periplasmic space

Sequence Length: 328 AAs

Molecular Weight: 36.003 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
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]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space
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:PS51318 , 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].

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].

Essentiality data for hybA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 4]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 5]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 4]

Subunit of hydrogenase 2: predicted hydrogenase 2 cytochrome b type component

Synonyms: HybB

Gene: hybB Accession Numbers: EG11800 (EcoCyc), 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 by computational analysis
GO:0017004 - cytochrome complex assembly Inferred by computational analysis
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0009055 - electron carrier activity Inferred by computational analysis
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: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].

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].

Essentiality data for hybB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 4]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 5]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 4]

Subunit of hydrogenase 2: hydrogenase 2, small subunit

Synonyms: YghV, HybO

Gene: hybO Accession Numbers: G7554 (EcoCyc), 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 by computational analysis
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Chan10, Chan09a, 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]
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: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 , Pfam:IN-FAMILY:PF01058 , Prints:IN-FAMILY:PR00614 , Prosite:IN-FAMILY:PS51318

Summary:
HybO is the small subunit of hydrogenase 2, and it contains three Fe-S centers [Sargent98a]. Hydrogenase 2 is associated with the periplasmic side of the cytoplasmic membrane [Ballantine86, Rodrigue96]. HybO contains a twin-arginine signal sequence which is required for membrane targeting by the Tat system [Sargent98a].

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

Review: [Vignais04]

Essentiality data for hybO knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 4]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 5]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 4]
Yes [Feist07, Comment 6]

Subunit of hydrogenase 2: hydrogenase 2, large subunit

Synonyms: HybC

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

Locations: periplasmic space, inner membrane

Sequence Length: 567 AAs

Molecular Weight: 62.491 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred by computational analysis
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0008901 - ferredoxin hydrogenase activity Inferred by computational analysis [GOA01a]
GO:0009055 - electron carrier activity Inferred by computational analysis
GO:0016151 - nickel cation binding Inferred by computational analysis [GOA01a]
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]
Cellular Component: GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a]
GO:0030288 - outer membrane-bounded periplasmic space

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

Isozyme Sequence Similarity:
hydrogenase 1, large subunit: YES

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 , Pfam:IN-FAMILY:PF00374 , Prosite:IN-FAMILY:PS00507 , Prosite:IN-FAMILY:PS00508

Summary:
HybC is the large subunit of hydrogenase 2. Hydrogenase 2 is associated with the periplasmic side of the cytoplasmic membrane [Ballantine86, Rodrigue96]. HybC is processed; N-terminal sequencing of the mature protein confirmed that processing does not occur at the N terminus [Sargent98a], while alteration of the C terminus of HybC interferes with processing [Zhang03d].

HybC and HybO are coordinately assembled and processed; the presence of both subunits, nickel acquisition and the subsequent processing of HybC, and the N-terminal signal sequence of HybO are required for export of both subunits by the Tat system [Rodrigue96, Rodrigue99].

Expression of the hyb operon is induced under anaerobic conditions and repressed by nitrate [Richard99].

Review: [Vignais04]

Essentiality data for hybC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 3]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 4]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 5]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 4]
Yes [Feist07, Comment 6]

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

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

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

Chan09a: 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.

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

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."

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

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

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

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

Sawers94: Sawers G (1994). "The hydrogenases and formate dehydrogenases of Escherichia coli." Antonie Van Leeuwenhoek 1994;66(1-3);57-88. PMID: 7747941

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."

Vignais04: Vignais PM, Colbeau A (2004). "Molecular biology of microbial hydrogenases." Curr Issues Mol Biol 6(2);159-88. PMID: 15119826

Zhang03d: 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 EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, biocyc14.