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MetaCyc Polypeptide: hydrogenase 2 - [Fe-S] binding, ferredoxin-type component HybA

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

Synonyms: hydL

Species: Escherichia coli K-12 substr. MG1655

Component of: hydrogenase 2 (extended summary available)

Summary:
The hybA-encoded protein may be involved in the periplasmic electron-transferring activity of hydrogenase 2 during catalytic turnover [Sargent98]. 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].

Locations: periplasmic space, cytosol, inner membrane

Map Position: [3,142,176 <- 3,143,162]

Molecular Weight of Polypeptide: 36.003 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009832 , CGSC:33407 , EchoBASE:EB1747 , EcoGene:EG11799 , EcoliWiki:b2996 , ModBase:P0AAJ8 , OU-Microarray:b2996 , PortEco:hybA , PR:PRO_000022948 , Protein Model Portal:P0AAJ8 , RefSeq:NP_417470 , RegulonDB:EG11799 , 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

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

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

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


Subunit of: 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, Sargent98]. 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, Sargent98, Rodrigue99, Zhang03k, 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

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, Sargent98, 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 [Sargent98]

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


Sequence Features

Feature Class Location Common Name Citations Comment
Signal-Sequence 1 -> 27  
[UniProt10]
UniProt: Tat-type signal; Non-Experimental Qualifier: potential;
Chain 28 -> 328  
[UniProt09]
UniProt: Hydrogenase-2 operon protein hybA;
Conserved-Region 38 -> 68  
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 1;
Conserved-Region 47 -> 58 cluster 1
[Menon94]
predicted [4Fe-4S] binding domain
Metal-Binding-Site 47  
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 50  
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 53  
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 57  
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 103 -> 134  
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 2;
Conserved-Region 112 -> 125 cluster 2
[Menon94]
predicted [3Fe-4S] binding domain
Metal-Binding-Site 112  
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 115  
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 120  
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 124  
[UniProt10]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 136 -> 165  
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 3;
Conserved-Region 145 -> 156 cluster 3
[Menon94]
predicted [4Fe-4S] binding domain
Metal-Binding-Site 145  
[UniProt10]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 148  
[UniProt10]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 151  
[UniProt10]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 155  
[UniProt10]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 174 -> 198 cluster 4
[Menon94]
predicted [4Fe-4S] binding domain
Metal-Binding-Site 174  
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 177  
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 193  
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 197  
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Alpha-Helix-Region 296 -> 311  
[Hatzixanthis03]
single C-terminal transmembrane helix

History:
10/20/97 Gene b2996 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11799; confirmed by SwissProt match.


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

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

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

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 H(2)-consuming over H(2)-evolving reactions during fermentative growth of Escherichia coli." BMC Microbiol 11;196. PMID: 21880124

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

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

Sargent98: 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

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

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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

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

Zhang03k: 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 Fri Jul 3, 2015, BIOCYC13A.