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Escherichia coli K-12 substr. MG1655 Polypeptide: hydrogenase 2, small subunit



Gene: hybO Accession Numbers: G7554 (EcoCyc), b2997, ECK2991

Synonyms: yghV, hyb0

Regulation Summary Diagram: ?

Component of: hydrogenase 2 (summary available)

Summary:
HybO is the small subunit of hydrogenase 2, and it contains three Fe-S centers [Sargent98]. 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 [Sargent98].

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]

Gene Citations: [Menon94]

Locations: inner membrane, periplasmic space

Map Position: [3,143,165 <- 3,144,283] (67.75 centisomes)
Length: 1119 bp / 372 aa

Molecular Weight of Polypeptide: 39.652 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009834 , DIP:DIP-36024N , EchoBASE:EB2828 , EcoGene:EG13006 , EcoliWiki:b2997 , Mint:MINT-8046452 , ModBase:P69741 , OU-Microarray:b2997 , PortEco:hybO , PR:PRO_000022953 , Protein Model Portal:P69741 , RefSeq:NP_417471 , RegulonDB:G7554 , 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

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred by computational analysis
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01a]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Chan10a, 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 [UniProtGOA11]
GO:0033748 - hydrogenase (acceptor) activity Inferred by computational analysis [GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11, GOA01a]
GO:0051538 - 3 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0016020 - membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11, Lasserre06]
GO:0005886 - plasma membrane Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, Rodrigue96]
GO:0009375 - ferredoxin hydrogenase complex Inferred by computational analysis [GOA01a]
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

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

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 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 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, Sargent98].

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

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 5], Ni2+ [Comment 6]

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


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 37
[Sargent98]
Cleavage of the signal peptide has been confirmed by N-terminal sequencing of the purified protein [Sargent98].
Chain 38 -> 372
[UniProt09]
UniProt: Hydrogenase-2 small chain;
Metal-Binding-Site 59
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 62
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 157
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 191
[UniProt10]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 229
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); via pros nitrogen; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 232
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 257
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 263
[UniProt10]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 272
[UniProt10]
UniProt: Iron-sulfur 3 (3Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 292
[UniProt10]
UniProt: Iron-sulfur 3 (3Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 295
[UniProt10]
UniProt: Iron-sulfur 3 (3Fe-4S); Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

Chan10a: 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

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

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

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

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 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

Other References Related to Gene Regulation

Chung13: Chung D, Park D, Myers K, Grass J, Kiley P, Landick R, Keles S (2013). "dPeak: high resolution identification of transcription factor binding sites from PET and SET ChIP-Seq data." PLoS Comput Biol 9(10);e1003246. PMID: 24146601

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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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