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Escherichia coli K-12 substr. MG1655 Polypeptide: predicted hydrogenase 2 cytochrome b type component



Gene: hybB Accession Numbers: EG11800 (EcoCyc), b2995, ECK2989

Regulation Summary Diagram: ?

Component of: hydrogenase 2 (summary available)

Summary:
The HybB protein is predicted to be an integral membrane component of hydrogenase 2 [Menon94].

A hybB in-frame deletion mutant can not grow on glycerol and fumarate as the sole energy sources. However, the HybOHybC complex is correctly targeted to the membrane and active with the artificial electron acceptor benzyl viologen (BV) [Dubini02].

Gene Citations: [Sargent98]

Locations: inner membrane

Map Position: [3,141,008 <- 3,142,186] (67.7 centisomes)
Length: 1179 bp / 392 aa

Molecular Weight of Polypeptide: 43.602 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009830 , CGSC:33414 , EchoBASE:EB1748 , EcoGene:EG11800 , EcoliWiki:b2995 , OU-Microarray:b2995 , PortEco:hybB , Protein Model Portal:P37180 , RefSeq:NP_417469 , RegulonDB:EG11800 , String:511145.b2995 , UniProt:P37180

Relationship Links: InterPro:IN-FAMILY:IPR005614 , Pfam:IN-FAMILY:PF03916

In Paralogous Gene Group: 245 (2 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009061 - anaerobic respiration Inferred by computational analysis
GO:0017004 - cytochrome complex assembly Inferred by computational analysis
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0009055 - electron carrier activity Inferred by computational analysis
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005886 - plasma membrane Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, DiazMejia09, Daley05]
GO:0016020 - membrane Inferred by computational analysis [UniProtGOA11]
GO:0016021 - integral component of membrane Inferred by computational analysis [UniProtGOA11]

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

Essentiality data for hybB 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]

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 4], Ni2+ [Comment 5]

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


Sequence Features

Feature Class Location Citations Comment
Transmembrane-Region 12 -> 32
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 35 -> 55
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 59 -> 79
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 91 -> 111
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 134 -> 154
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 169 -> 189
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 208 -> 228
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 250 -> 270
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 282 -> 302
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Sequence-Conflict 306 -> 307
[Menon94, UniProt10a]
Alternate sequence: KL → NV; UniProt: (in Ref. 1; AAA21590/AAA69162);
Transmembrane-Region 334 -> 354
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;
Transmembrane-Region 356 -> 376
[UniProt10]
UniProt: Helical;; Non-Experimental Qualifier: potential;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b2995 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11800; 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

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

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

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.

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

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

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

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

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 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."

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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Nov 24, 2014, BIOCYC13B.