Escherichia coli K-12 substr. MG1655 Polypeptide: hydrogenase 1, large subunit

Gene: hyaB Accession Numbers: EG10469 (EcoCyc), b0973, ECK0964

Regulation Summary Diagram: ?

Regulation summary diagram for hyaB

Component of: hydrogenase 1 (extended summary available)

HyaB is the large subunit of hydrogenase 1; it is thought to bind the Ni-Fe active site cofactor. Processing of HyaB at the C terminus is required for the formation of active hydrogenase [Menon91]; the cleavage is proposed to take place at the conserved His582 residue [Menon93]. Nickel binding is one of the requirements for C terminal processing of the large subunit [Przybyla92].

Expression of the hya operon is induced under anaerobic conditions and by the presence of formate, but repressed by nitrate [Brondsted94, Richard99]. Expression is increased under acidic conditions [King99].

A hyaB in-frame deletion mutant does not have a defect in anaerobic growth with hydrogen and fumarate as sole energy and carbon sources, while a hyaB hybC double mutant did not grow under these conditions [Dubini02].

Review: [Vignais04]

Gene Citations: [Menon90, Maciag11]

Locations: periplasmic space, inner membrane

Map Position: [1,032,477 -> 1,034,270] (22.25 centisomes, 80°)
Length: 1794 bp / 597 aa

Molecular Weight of Polypeptide: 66.253 kD (from nucleotide sequence)

pI: 6.04

Isozyme Sequence Similarity:
hydrogenase 2, large subunit: YES

Unification Links: ASAP:ABE-0003288 , CGSC:31784 , DIP:DIP-36180N , EchoBASE:EB0464 , EcoGene:EG10469 , EcoliWiki:b0973 , ModBase:P0ACD8 , OU-Microarray:b0973 , PortEco:hyaB , PR:PRO_000022944 , Protein Model Portal:P0ACD8 , RefSeq:NP_415492 , RegulonDB:EG10469 , SMR:P0ACD8 , String:511145.b0973 , UniProt:P0ACD8

Relationship Links: InterPro:IN-FAMILY:IPR001501 , InterPro:IN-FAMILY:IPR018194 , InterPro:IN-FAMILY:IPR029014 , PDB:Structure:3UQY , PDB:Structure:3USC , PDB:Structure:3USE , PDB:Structure:4GD3 , Pfam:IN-FAMILY:PF00374 , Prosite:IN-FAMILY:PS00507 , Prosite:IN-FAMILY:PS00508

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for hyaB

GO Terms:

Biological Process: GO:0009060 - aerobic respiration
GO:0009061 - anaerobic respiration
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0008901 - ferredoxin hydrogenase activity Inferred by computational analysis [GOA01]
GO:0009055 - electron carrier activity
GO:0016151 - nickel cation binding Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11]
GO:0033748 - hydrogenase (acceptor) activity Inferred by computational analysis [GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, Menon91, Lasserre06]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]
GO:0030288 - outer membrane-bounded periplasmic space Inferred by computational analysis [DiazMejia09]

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

Essentiality data for hyaB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

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)

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:

Transport reaction diagram for hydrogenase

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 5, DerVartanian96, Sawers86]

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

Kinetic Parameters:

Km (μM)

Sequence Features

Protein sequence of hydrogenase 1, large subunit with features indicated

Feature Class Location Citations Comment
Sequence-Conflict 52
[Menon90, UniProt10]
UniProt: (in Ref. 1; AAA23998);
Sequence-Conflict 69
[Menon90, UniProt10]
UniProt: (in Ref. 1; AAA23998);
Metal-Binding-Site 76
UniProt: Nickel; Non-Experimental Qualifier: potential;
Metal-Binding-Site 79
UniProt: Nickel; Non-Experimental Qualifier: potential;
Metal-Binding-Site 576
UniProt: Nickel; Non-Experimental Qualifier: potential;
Metal-Binding-Site 579
UniProt: Nickel; Non-Experimental Qualifier: potential;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b0973 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10469; confirmed by SwissProt match.


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

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

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

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

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

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

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

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

Maciag11: 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

Menon93: Menon NK, Robbins J, Der Vartanian M, Patil D, Peck HD, Menon AL, Robson RL, Przybyla AE (1993). "Carboxy-terminal processing of the large subunit of [NiFe] hydrogenases." FEBS Lett 331(1-2);91-5. PMID: 8405419

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

Przybyla92: Przybyla AE, Robbins J, Menon N, Peck HD (1992). "Structure-function relationships among the nickel-containing hydrogenases." FEMS Microbiol Rev 1992;8(2);109-35. PMID: 1558764

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms 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

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

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

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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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