Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

MetaCyc Polypeptide: hydrogenase 2 4Fe-4S ferredoxin-type component

Gene: hybA Accession Numbers: EG11799 (MetaCyc), b2996, ECK2990

Synonyms: hydL

Species: Escherichia coli K-12 substr. MG1655

Component of: hydrogenase 2 (summary available)

Summary:
The hybA-encoded protein may be involved in the periplasmic electron-transferring activity of hydrogenase 2 during catalytic turnover [Sargent98].

An hybA in-frame deletion mutant can not grow on glycerol and fumarate as the sole energy sources, and its reduced fumarate-dependent hydrogen uptake activity is comparable to a hybC deletion mutant. However, the HybOHybC complex is correctly targeted to the membrane [Dubini02].

Locations: periplasmic space

Map Position: [3,142,176 <- 3,143,162]

Molecular Weight of Polypeptide: 36.003 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009832 , CGSC:33407 , EchoBASE:EB1747 , EcoGene:EG11799 , EcoliWiki:b2996 , ModBase:P0AAJ8 , OU-Microarray:b2996 , PortEco:hybA , PR:PRO_000022948 , Protein Model Portal:P0AAJ8 , RefSeq:NP_417470 , RegulonDB:EG11799 , SMR:P0AAJ8 , String:511145.b2996 , UniProt:P0AAJ8

Relationship Links: InterPro:IN-FAMILY:IPR001450 , InterPro:IN-FAMILY:IPR017896 , InterPro:IN-FAMILY:IPR017900 , InterPro:IN-FAMILY:IPR019546 , Pfam:IN-FAMILY:PF00037 , Pfam:IN-FAMILY:PF12798 , Pfam:IN-FAMILY:PF12838 , Prosite:IN-FAMILY:PS00198 , Prosite:IN-FAMILY:PS51318 , Prosite:IN-FAMILY:PS51379

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0051536 - iron-sulfur cluster binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0051539 - 4 iron, 4 sulfur cluster binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space Inferred by computational analysis [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: metabolism energy production/transport electron donors

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Subunit of: hydrogenase 2

Synonyms: HYD2, hydrogenase-2

Species: Escherichia coli K-12 substr. MG1655

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]

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


Enzymatic reaction of: hydrogenase

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

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 1], Ni2+ [Comment 2]

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


Sequence Features

Feature Class Location Citations Comment
Signal-Sequence 1 -> 27
[UniProt10a]
UniProt: Tat-type signal; Non-Experimental Qualifier: potential;
Chain 28 -> 328
[UniProt09]
UniProt: Hydrogenase-2 operon protein hybA;
Conserved-Region 38 -> 68
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 1;
Metal-Binding-Site 47
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 50
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 53
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 57
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 103 -> 134
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 2;
Metal-Binding-Site 112
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 115
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 120
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 124
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Conserved-Region 136 -> 165
[UniProt09]
UniProt: 4Fe-4S ferredoxin-type 3;
Metal-Binding-Site 145
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 148
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 151
[UniProt10a]
UniProt: Iron-sulfur 4 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 155
[UniProt10a]
UniProt: Iron-sulfur 3 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 174
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 177
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 193
[UniProt10a]
UniProt: Iron-sulfur 2 (4Fe-4S); Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 197
[UniProt10a]
UniProt: Iron-sulfur 1 (4Fe-4S); Non-Experimental Qualifier: by similarity;

History:
10/20/97 Gene b2996 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11799; confirmed by SwissProt match.


References

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

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.

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

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

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

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.

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."


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
Page generated by SRI International Pathway Tools version 18.5 on Fri Nov 28, 2014, BIOCYC13B.