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Escherichia coli K-12 substr. MG1655 Polypeptide: hydrogenase 1, b-type cytochrome subunit



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

Synonyms: cybH

Regulation Summary Diagram: ?

Regulation summary diagram for hyaC

Component of: hydrogenase 1 (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, although resulting in the appearance of multiple forms of the enzyme [Menon91].

Review: [Vignais04]

Gene Citations: [Maciag11a]

Locations: inner membrane

Map Position: [1,034,289 -> 1,034,996] (22.29 centisomes, 80°)
Length: 708 bp / 235 aa

Molecular Weight of Polypeptide: 27.597 kD (from nucleotide sequence)

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

Reactions known to consume the compound:

Not in pathways:
a ubiquinol-8 oxidoreductase + a b-type cytochrome → a ubiquinone-8 oxidoreductase + a reduced b-type cytochrome
a b-type cytochrome + a menaquinone oxidoreductase (demethylmenaquinol) → a reduced b-type cytochrome + a menaquinone oxidoreductase (demethylmenaquinone)
a b-type cytochrome + a menaquinone oxidoreductase (menaquinol-8) → a reduced b-type cytochrome + a menaquinone oxidoreductase (menaquinone-8)
a reduced b-type cytochrome + a b-type cytochromea b-type cytochrome + a reduced cytochrome o

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for hyaC

GO Terms:

Biological Process: GO:0006810 - transport Inferred by computational analysis [GOA01a]
GO:0009060 - aerobic respiration
GO:0009061 - anaerobic respiration
GO:0022904 - respiratory electron transport chain Inferred by computational analysis [GOA01a]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0005506 - iron ion binding Inferred by computational analysis [GOA01a]
GO:0009055 - electron carrier activity Inferred by computational analysis [GOA01a]
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, 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

Essentiality data for hyaC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 1]
Yes [Feist07, Comment 3]

Subunit of: hydrogenase 1

Synonyms: HYD1, hydrogenase I, NiFe hydrogenase

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

Summary:
Hydrogenase 1 mediates hydrogen uptake in the presence of high-potential acceptors such as ferricyanide and phenazine methosulfate, but not low-potential acceptors [Laurinavichene01]. The enzyme is more tolerant to oxygen than hydrogenase 2, providing complementary redox properties to the cell [Laurinavichene02, Lukey10, Wulff14].

Hydrogenase 1 contains a [3Fe-4S] or [4Fe-4S] cluster (depending on oxidation state) and nickel [DerVartanian96]. The substrate specificity of hydrogenase 1 for various quinones is unknown [Laurinavichene01].

HybG [Blokesch01] and HybF [Hube02] are involved in maturation of hydrogenase 1.

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]

Locations: membrane

GO Terms:

Molecular Function: GO:0016151 - nickel cation binding Inferred from experiment [DerVartanian96]
GO:0051536 - iron-sulfur cluster binding Inferred from experiment [DerVartanian96]
Cellular Component: GO:0016020 - membrane [Ballantine85]


Enzymatic reaction of: hydrogenase

Synonyms: hydrogenlyase

EC Number: 1.12.99.6

Transport reaction diagram for hydrogenase

Summary:
There are four hydrogenases in E. coli which are synthesized in response to different physiological conditions. Hydrogenase 1 is a membrane-bound nickel-containing protein [Menon90, Sawers94]. It contains as electron-transfer components Fe-S clusters and nickel. It catalyzes the oxidation of hydrogen; the physiological electron carrier is unknown. The enzyme effects proton translocation coupled to the scalar redox reaction. [Sawers86]

Cofactors or Prosthetic Groups: [FeS] iron-sulfur cluster [DerVartanian96], Ni2+ [Comment 4, DerVartanian96, Sawers86]

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

Kinetic Parameters:

Substrate
Km (μM)
Citations
H2
2.0
[Sawers86]


Sequence Features

Protein sequence of hydrogenase 1, b-type cytochrome subunit with features indicated

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;
Transmembrane-Region 186 -> 203
[UniProt10a]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram

Notes:

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


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

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

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

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

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

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

Maciag11a: Maciag A, Peano C, Pietrelli A, Egli T, De Bellis G, Landini P (2011). "In vitro transcription profiling of the {sigma}S subunit of bacterial RNA polymerase: re-definition of the {sigma}S regulon and identification of {sigma}S-specific promoter sequence elements." Nucleic Acids Res 39(13);5338-55. PMID: 21398637

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

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

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

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

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

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

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

Other References Related to Gene Regulation

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

Bradley07: Bradley MD, Beach MB, de Koning AP, Pratt TS, Osuna R (2007). "Effects of Fis on Escherichia coli gene expression during different growth stages." Microbiology 153(Pt 9);2922-40. PMID: 17768236

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

Giel06: Giel JL, Rodionov D, Liu M, Blattner FR, Kiley PJ (2006). "IscR-dependent gene expression links iron-sulphur cluster assembly to the control of O-regulated genes in Escherichia coli." Mol Microbiol 60(4);1058-75. PMID: 16677314

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

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

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


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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