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MetaCyc Polypeptide: hydrogenase 1, b-type cytochrome subunit

Gene: hyaC Accession Numbers: EG10470 (MetaCyc), b0974, ECK0965

Synonyms: cybH, hydrogenase 1 - B subunit, hydrogenase 1 - γ subunit

Species: Escherichia coli K-12 substr. MG1655

Component of:
hydrogenase 1
hydrogenase 1, oxygen tolerant hydrogenase (extended summary available)

Summary:
The hyaC gene product is very hydrophobic, rich in aromatic residues, and has four putative hydrophobic membrane-spanning regions [Menon90].

An in-frame deletion in the hyaC gene results in wild-type levels of hydrogenase 1 activity and the appearance of multiple forms of the enzyme during purification [Menon91]. Sequence analysis suggests that the HyaC subunit contains two heme groups but only one heme could be identified in the crystal structure of the hydrogenase 1 complex; HyaC's main function may be anchoring the hydrogenase to the membrane [Volbeda13].

Locations: inner membrane

Map Position: [1,034,289 -> 1,034,996]

Molecular Weight of Polypeptide: 27.597 kD (from nucleotide sequence), 26.0 kD (experimental) [Menon91 ]

pI: 9.42

Unification Links: ASAP:ABE-0003290 , CGSC:31788 , DIP:DIP-35859N , EchoBASE:EB0465 , EcoGene:EG10470 , EcoliWiki:b0974 , ModBase:P0AAM1 , OU-Microarray:b0974 , PortEco:hyaC , Protein Model Portal:P0AAM1 , RefSeq:NP_415493 , RegulonDB:EG10470 , SMR:P0AAM1 , String:511145.b0974 , UniProt:P0AAM1

Relationship Links: InterPro:IN-FAMILY:IPR000516 , InterPro:IN-FAMILY:IPR011577 , InterPro:IN-FAMILY:IPR016174 , PDB:Structure:4GD3 , Pfam:IN-FAMILY:PF00033 , Pfam:IN-FAMILY:PF01292 , Prints:IN-FAMILY:PR00161 , Prosite:IN-FAMILY:PS00882 , Prosite:IN-FAMILY:PS00883

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0006113 - fermentation Inferred from experiment [Brondsted94]
GO:0009061 - anaerobic respiration Inferred from experiment [Brondsted94]
GO:0006810 - transport Inferred by computational analysis [GOA01a]
GO:0019645 - anaerobic electron transport chain Inferred by curator [Laurinavichene01]
GO:0022904 - respiratory electron transport chain Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
GO:1902421 - hydrogen metabolic process Inferred by curator [Laurinavichene01, Sawers86]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Volbeda13]
GO:0020037 - heme binding Inferred from experiment [Volbeda13]
GO:0005506 - iron ion binding Inferred by computational analysis [GOA01a]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01a]
GO:0033748 - hydrogenase (acceptor) activity Inferred by curator [Sawers86]
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, Daley05, DiazMejia09]
GO:0005887 - integral component of plasma membrane Inferred by computational analysis Inferred from experiment [Volbeda13, Menon90]
GO:0044569 - [Ni-Fe] hydrogenase complex Inferred from experiment [Volbeda13]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11a, GOA01a]

MultiFun Terms: cell structure membrane
metabolism biosynthesis of macromolecules (cellular constituents) large molecule carriers cytochromes
metabolism energy metabolism, carbon aerobic respiration
metabolism energy metabolism, carbon anaerobic respiration
metabolism energy production/transport electron donors

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


Subunit of: hydrogenase 1

Synonyms: HYD1, hydrogenase I, NiFe hydrogenase, hydrogen:menaquinone oxidoreductase, hydrogen oxidase, hydrogen:oxygen oxidoreductase

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of hydrogenase 1 = [HyaA]2[HyaB]2[HyaC]
         hydrogenase 1, small subunit = HyaA (extended summary available)
         hydrogenase 1, large subunit = HyaB (summary available)
         hydrogenase 1, b-type cytochrome subunit = HyaC (summary available)

Component of: hydrogenase 1, oxygen tolerant hydrogenase (extended summary available)

Relationship Links: PDB:Structure:3UQY , PDB:Structure:3USC , PDB:Structure:3USE

Credits:
Revised in EcoCyc 19-Feb-2015 by Mackie A , Macquarie University
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International


Subunit of: hydrogenase 1, oxygen tolerant hydrogenase

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of hydrogenase 1, oxygen tolerant hydrogenase = [(HyaA)2(HyaB)2(HyaC)]2
         hydrogenase 1 = (HyaA)2(HyaB)2(HyaC)
                 hydrogenase 1, small subunit = HyaA (extended summary available)
                 hydrogenase 1, large subunit = HyaB (summary available)
                 hydrogenase 1, b-type cytochrome subunit = HyaC (summary available)

Summary:
Hydrogenase I (encoded by the hyaABC genes in E. coli K-12) is an oxygen-tolerant, membrane bound Ni-Fe hydrogenase [Sawers86, Laurinavichene01]. The purified enzyme catalyses H2:benzyl viologen oxidoreduction; it also catalyses H2 evolution with methyl viologen as an electron donor [Sawers86]. In a strain lacking the hydrogenase 2 enzyme, hydrogenase 1 catalyses nitrate dependent H2 consumption and DMSO dependent H2 consumption but is less active with methyl viologen, benzyl viologen and fumarate. This mutant strain also demonstrates H2 consumption in the presence of air (ie. it is active in the Knallgas reaction 2H2 + O2 → 2H2O); hydrogenase 1 donates electrons preferentially to acceptors with higher reduction potential and is active at higher oxygen concentrations than hydrogenase 2 [Laurinavichene01, Laurinavichene02].

Purified hydrogenase 1 is a uni-directional, oxygen-tolerant H(2) oxidizer; hydrogenase 1 may function as an energy conserving, H(2) scavenger under conditions of slow growth and fluctuating oxygen levels [Lukey10]. Hydrogenase 1 can directly catalyse the 4 electron reduction of oxygen to water using H(2) as donor; when hydrogenase 1 reacts exclusively with H(2) and oxygen, 86% of the water produced arises from this direct reaction [Wulff14]. The oxidase activity of of hydrogenase 1 is low and serves to protect the active site from oxygen attack [Wulff14]

The membrane bound complex crystallises as a [HyaC(HyaAHyaB)2]2 complex and this is thought to be the physiologically relevant structure. Hydrogenase I is anchored to the membrane by both a HyaA C-terminal helix and an inner membrane b-type cytochome, HyaC; cytochrome b's main role may be anchoring the heterodimer (HyaAB) to the membrane. The small subunit (HyaA) contains a distal [4Fe-4S]cluster, a medial [3Fe-4S] cluster and a unique proximal [4Fe-3S] cluster; the large subunit (HyaB) contains the Ni-Fe active site [Volbeda12, Volbeda13].

The basis of hydrogenase 1 oxygen tolerance is that all electrons required to directly reduce H(2) to water are readily available and can be rapidly transferred back to the active Ni-Fe site upon oxygen attack; this relies upon the unique properties of the proximal [4Fe-3S] cluster and the presence of a high potential medial [3Fe-4S] cluster [Lukey11, Roessler12, Evans13] (and see [Cracknell09, Parkin12]).

The physiological function of hydrogenase 1 is uncertain. Hydrogenase 1 and cytochrome bd-II terminal oxidase may constitute a respiratory chain between H(2) and oxygen that functions under microaerobic conditions [Atlung97, Wulff14]. Hydrogenase 1 may function in 'aerobic shock protection' - that is, it may function to keep intracellular O2 levels low (by reducing it to water), thus protecting O2-sensitive enzymes during the anaerobic to aerobic transition [Volbeda13].

The substrate specificity of hydrogenase 1 for various quinones is unknown [Laurinavichene01].

Maturation and membrane targeting of hydrogenase 1 involves proteins encoded within the hyp (HypB, HypD, HypE), hya (HyaD, HyaE, HyaF) and hyb operons (HybF, HybG) and the HypF protein (reviewed in: [Bock06, Forzi07]).

Hydrogenase 1 content is increased during fermentation in the presence of formate [Sawers85]. Expression of the hya operon is induced under anaerobic conditions and in the presence of formate, but repressed by nitrate [Brondsted94, Richard99]. hya expresssion is repressed aerobically by the IscR repressor; AppY and ArcA prevent IscR repression under anaerobic conditions [Nesbit12]

E. coli K-12 contains a second respiratory hydrogenase - hydrogenase 2 - 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. Only hydrogenase 1 can reduce nitroblue tetrazolium in anaerobically growing E. coli cells [Pinske12].

Review: [Vignais04]

Citations: [Pinske11, Ballantine85, DerVartanian96, King99, Blokesch01, Hube02]

Locations: periplasmic space, inner membrane

Relationship Links: PDB:Structure:4GD3

GO Terms:

Biological Process: GO:0006113 - fermentation Inferred from experiment [Sawers85]
GO:0009061 - anaerobic respiration Inferred from experiment [Ballantine85, Brondsted94]
GO:0019645 - anaerobic electron transport chain Inferred from experiment [Laurinavichene01]
GO:1902421 - hydrogen metabolic process Inferred from experiment [Sawers86, Laurinavichene01]
Molecular Function: GO:0009055 - electron carrier activity Inferred from experiment [Volbeda12, Laurinavichene01]
GO:0016151 - nickel cation binding Inferred from experiment [Sawers86, DerVartanian96]
GO:0020037 - heme binding Inferred from experiment [Volbeda13]
GO:0033748 - hydrogenase (acceptor) activity Inferred from experiment [Sawers86, Lukey10, Menon91]
GO:0051536 - iron-sulfur cluster binding Inferred from experiment [Sawers86, DerVartanian96]
Cellular Component: GO:0031237 - intrinsic component of periplasmic side of plasma membrane Inferred from experiment [Volbeda13]
GO:0044569 - [Ni-Fe] hydrogenase complex Inferred by computational analysis Inferred from experiment [Volbeda13, DerVartanian96, Sawers86, Menon90]

Credits:
Created in EcoCyc 23-Feb-2015 by Mackie A , Macquarie University
Imported from EcoCyc 02-Jun-2015 by Paley S , SRI International


Enzymatic reaction of: hydrogen:menaquinone oxidoreductase (hydrogenase 1, oxygen tolerant hydrogenase)

Synonyms: hydrogenlyase

Transport reaction diagram for hydrogen:menaquinone oxidoreductase

In Pathways: 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 1 complex depicts the transfer of electrons to menaquinone in the inner membrane. This representation has not been experimentally established and is therefore speculative.

Cofactors or Prosthetic Groups: ferroheme b [Volbeda13], a [4Fe-3S] iron-sulfur cluster [Volbeda12], a [4Fe-4S] iron-sulfur cluster [Volbeda12, DerVartanian96], a [3Fe-4S] iron-sulfur cluster [Volbeda12, DerVartanian96], a nickel-iron-sulfur cluster [Volbeda12, Sawers86, DerVartanian96]

Inhibitors (Unknown Mechanism): carbon monoxide [Sawers86] , azide [Sawers86] , N-bromosuccinimide [Sawers86]

Kinetic Parameters:

Substrate
Km (μM)
Citations
H2
2.0
[Sawers86]


Enzymatic reaction of: hydrogen:oxygen oxidoreductase (hydrogenase 1, oxygen tolerant hydrogenase)

2 H2 + oxygen <=> 2 H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

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


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 20 -> 40
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 64 -> 84
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 131 -> 151
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Metal-Binding-Site 181
[Volbeda13]
heme b ligand
Transmembrane-Region 186 -> 203
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;

History:
10/20/97 Gene b0974 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10470; confirmed by SwissProt match.


References

Atlung97: Atlung T, Knudsen K, Heerfordt L, Brondsted L (1997). "Effects of sigmaS and the transcriptional activator AppY on induction of the Escherichia coli hya and cbdAB-appA operons in response to carbon and phosphate starvation." J Bacteriol 179(7);2141-6. PMID: 9079897

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

Blokesch01: Blokesch M, Magalon A, Bock A (2001). "Interplay between the specific chaperone-like proteins HybG and HypC in maturation of hydrogenases 1, 2, and 3 from Escherichia coli." J Bacteriol 183(9);2817-22. PMID: 11292801

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

Brondsted94: Brondsted L, Atlung T (1994). "Anaerobic regulation of the hydrogenase 1 (hya) operon of Escherichia coli." J Bacteriol 176(17);5423-8. PMID: 8071220

Cracknell09: Cracknell JA, Wait AF, Lenz O, Friedrich B, Armstrong FA (2009). "A kinetic and thermodynamic understanding of O2 tolerance in [NiFe]-hydrogenases." Proc Natl Acad Sci U S A 106(49);20681-6. PMID: 19934053

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

DerVartanian96: DerVartanian ME, Menon NK, Przybyla AE, Peck HD, DerVartanian DV (1996). "Electron paramagnetic resonance (EPR) studies on hydrogenase-1 (HYD1) purified from a mutant strain (AP6) of Escherichia coli enhanced in HYD1." Biochem Biophys Res Commun 227(1);211-5. PMID: 8858127

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

Evans13: Evans RM, Parkin A, Roessler MM, Murphy BJ, Adamson H, Lukey MJ, Sargent F, Volbeda A, Fontecilla-Camps JC, Armstrong FA (2013). "Principles of sustained enzymatic hydrogen oxidation in the presence of oxygen--the crucial influence of high potential Fe-S clusters in the electron relay of [NiFe]-hydrogenases." J Am Chem Soc 135(7);2694-707. PMID: 23398301

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Hube02: Hube M, Blokesch M, Bock A (2002). "Network of hydrogenase maturation in Escherichia coli: role of accessory proteins HypA and HybF." J Bacteriol 184(14);3879-85. PMID: 12081959

King99: King PW, Przybyla AE (1999). "Response of hya expression to external pH in Escherichia coli." J Bacteriol 181(17);5250-6. PMID: 10464194

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

Lukey11: Lukey MJ, Roessler MM, Parkin A, Evans RM, Davies RA, Lenz O, Friedrich B, Sargent F, Armstrong FA (2011). "Oxygen-tolerant [NiFe]-hydrogenases: the individual and collective importance of supernumerary cysteines at the proximal Fe-S cluster." J Am Chem Soc 133(42);16881-92. PMID: 21916508

Menon90: Menon NK, Robbins J, Peck HD, Chatelus CY, Choi ES, Przybyla AE (1990). "Cloning and sequencing of a putative Escherichia coli [NiFe] hydrogenase-1 operon containing six open reading frames." J Bacteriol 1990;172(4);1969-77. PMID: 2180913

Menon91: Menon NK, Robbins J, Wendt JC, Shanmugam KT, Przybyla AE (1991). "Mutational analysis and characterization of the Escherichia coli hya operon, which encodes [NiFe] hydrogenase 1." J Bacteriol 173(15);4851-61. PMID: 1856178

Nesbit12: Nesbit AD, Fleischhacker AS, Teter SJ, Kiley PJ (2012). "ArcA and AppY antagonize IscR repression of hydrogenase-1 expression under anaerobic conditions, revealing a novel mode of O2 regulation of gene expression in Escherichia coli." J Bacteriol 194(24);6892-9. PMID: 23065979

Parkin12: Parkin A, Sargent F (2012). "The hows and whys of aerobic H2 metabolism." Curr Opin Chem Biol 16(1-2);26-34. PMID: 22366384

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

Pinske12: Pinske C, Jaroschinsky M, Sargent F, Sawers G (2012). "Zymographic differentiation of [NiFe]-hydrogenases 1, 2 and 3 of Escherichia coli K-12." BMC Microbiol 12;134. PMID: 22769583

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

Roessler12: Roessler MM, Evans RM, Davies RA, Harmer J, Armstrong FA (2012). "EPR spectroscopic studies of the Fe-S clusters in the O2-tolerant [NiFe]-hydrogenase Hyd-1 from Escherichia coli and characterization of the unique [4Fe-3S] cluster by HYSCORE." J Am Chem Soc 134(37);15581-94. PMID: 22900997

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

Sawers86: Sawers RG, Boxer DH (1986). "Purification and properties of membrane-bound hydrogenase isoenzyme 1 from anaerobically grown Escherichia coli K12." Eur J Biochem 1986;156(2);265-75. PMID: 3516689

UniProt10a: 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

Volbeda12: Volbeda A, Amara P, Darnault C, Mouesca JM, Parkin A, Roessler MM, Armstrong FA, Fontecilla-Camps JC (2012). "X-ray crystallographic and computational studies of the O2-tolerant [NiFe]-hydrogenase 1 from Escherichia coli." Proc Natl Acad Sci U S A 109(14);5305-10. PMID: 22431599

Volbeda13: Volbeda A, Darnault C, Parkin A, Sargent F, Armstrong FA, Fontecilla-Camps JC (2013). "Crystal structure of the O(2)-tolerant membrane-bound hydrogenase 1 from Escherichia coli in complex with its cognate cytochrome b." Structure 21(1);184-90. PMID: 23260654

Wulff14: Wulff P, Day CC, Sargent F, Armstrong FA (2014). "How oxygen reacts with oxygen-tolerant respiratory [NiFe]-hydrogenases." Proc Natl Acad Sci U S A 111(18);6606-11. PMID: 24715724


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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