2.02012-05-31 13:50:50 -06002015-09-17 16:24:07 -0600ECMDB01362M2MDB000355Hydrogen (gas)Hydrogen is a colorless, odorless, nonmetallic, tasteless, highly flammable diatomic gas with the molecular formula H2. With an atomic weight of 1.00794, hydrogen is the lightest element. Besides the common H1 isotope, hydrogen exists as the stable isotope Deuterium and the unstable, radioactive isotope Tritium. Hydrogen is the most abundant of the chemical elements, constituting roughly 75% of the universe's elemental mass. Hydrogen can form compounds with most elements and is present in water and most organic compounds. It plays a particularly important role in acid-base chemistry, in which many reactions involve the exchange of protons between soluble molecules. Oxidation of hydrogen, in the sense of removing its electron, formally gives H+, containing no electrons and a nucleus which is usually composed of one proton. That is why H+ is often called a proton. This species is central to discussion of acids. Under the Bronsted-Lowry theory, acids are proton donors, while bases are proton acceptors. The transport of protons or hydrogen ions across the membrane(ie the creation of a proton gradient) is critical to the generation of energy (ATP) for all living cells.DihydrogenHydrogenHydrogen cationHydrogen gasHydrogen ionHydrogen moleculeHydroniumProtonH22.01592.015650064dihydrogendihydrogen1333-74-0[H][H]InChI=1S/H2/h1HUFHFLCQGNIYNRP-UHFFFAOYSA-NLiquidCytosolExtra-organismPeriplasmmelting_point-259.2 oCiupacdihydrogenaverage_mass2.0159mono_mass2.015650064smiles[H][H]formulaH2inchiInChI=1S/H2/h1HinchikeyUFHFLCQGNIYNRP-UHFFFAOYSA-Npolar_surface_area0refractivity0polarizability0.74rotatable_bond_count0acceptor_count0donor_count0physiological_charge0formal_charge0Methane metabolismec00680Trinitrotoluene degradationec00633Microbial metabolism in diverse environmentsec011202,3-dihydroxybenzoate biosynthesis2,3-dihydroxybenzoate is synthesized from chorismate via isochorismate and 2,3-dihydroxy-2,3-dihydrobenzoate. Chorismate is a key intermediate and branch point in the biosynthesis of many aromatic compounds.
The biosynthesis of 2,3-dihydroxybenzoate from chorismate is catalyzed by three enzymes EntC, EntB, and EntA. EntC catalyzes the conversion of chorismate to isochorismate. The N-terminal isochorismate lyase domain of EntB hydrolyzes the pyruvate group of isochorismate to produce 2,3-dihydro-2,3-dihydroxybenzoate. The conversion of this latter compound to 2,3-dihydroxybenzoate is catalyzed by the EntA dehydrogenase.
PW000751MetabolicMenaquinol biosythesisMenaquinol biosynthesis starts with chorismate being metabolized into isochorismate through a isochorismate synthase. Isochorismate then interacts with 2-oxoglutare and a hydrogen ion through a 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase resulting in the release of a carbon dioxide and a 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate. The latter compound then interacts with (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase resulting in the release of a pyruvate and a (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate. This compound is the dehydrated through a o-succinylbenzoate synthase resulting in the release of a water molecule and a 2-succinylbenzoate. This compound then interacts with a coenzyme A and an ATP through a o-succinylbenzoate CoA ligase resulting in the release of a diphosphate, a AMP and a succinylbenzoyl-CoA. The latter compound interacts with a hydrogen ion through a 1,4-dihydroxy-2-naphthoyl-CoA synthase resulting in the release of a water molecule or a 1,4-dihydroxy-2-naphthoyl-CoA. This compound then interacts with water through a 1,4-dihydroxy-2-naphthoyl-CoA thioesterase resulting in the release of a coenzyme A, a hydrogen ion and a 1,4-dihydroxy-2-naphthoate.
The 1,4-dihydroxy-2-naphthoate can interact with either farnesylfarnesylgeranyl-PP or octaprenyl diphosphate and a hydrogen ion through a 1,4-dihydroxy-2-naphthoate octaprenyltransferase resulting in a release of a carbon dioxide, a pyrophosphate and a demethylmenaquinol-8. This compound then interacts with SAM through a bifunctional 2-octaprenyl-6-methoxy-1,4-benzoquinone methylase and S-adenosylmethionine:2-DMK methyltransferase resulting in a hydrogen ion, a s-adenosyl-L-homocysteine and a menaquinol.PW001897Metabolicmixed acid fermentationFERMENTATION-PWYrespiration (anaerobic)ANARESP1-PWYSpecdb::MsMs24629Specdb::MsMs24630Specdb::MsMs24631Specdb::MsMs31187Specdb::MsMs31188Specdb::MsMs31189HMDB0136253625494515072C0028229235HYDROGEN-MOLECULEHydrogenKeseler, I. M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A. G., Mackie, A., Paulsen, I., Gunsalus, R. P., Karp, P. D. (2011). "EcoCyc: a comprehensive database of Escherichia coli biology." Nucleic Acids Res 39:D583-D590.21097882Kanehisa, M., Goto, S., Sato, Y., Furumichi, M., Tanabe, M. (2012). "KEGG for integration and interpretation of large-scale molecular data sets." Nucleic Acids Res 40:D109-D114.22080510Ait-Ichou, I.; Formenti, M.; Pommier, B.; Teichner, S. J. Photocatalytic dehydrogenation of isopropanol on platinum/titania catalysts. Journal of Catalysis (1985), 91(2), 293-307.Alkaline phosphataseP00634PPB_ECOLIphoAhttp://ecmdb.ca/proteins/P00634.xmlFormate dehydrogenase HP07658FDHF_ECOLIfdhFhttp://ecmdb.ca/proteins/P07658.xmlFormate hydrogenlyase subunit 2P0AAK1HYCB_ECOLIhycBhttp://ecmdb.ca/proteins/P0AAK1.xmlHydrogenase-1 large chainP0ACD8MBHL_ECOLIhyaBhttp://ecmdb.ca/proteins/P0ACD8.xmlHydrogenase-2 large chainP0ACE0MBHM_ECOLIhybChttp://ecmdb.ca/proteins/P0ACE0.xmlFormate hydrogenlyase subunit 5P16431HYCE_ECOLIhycEhttp://ecmdb.ca/proteins/P16431.xmlFormate hydrogenlyase subunit 6P16432HYCF_ECOLIhycFhttp://ecmdb.ca/proteins/P16432.xmlFormate hydrogenlyase subunit 7P16433HYCG_ECOLIhycGhttp://ecmdb.ca/proteins/P16433.xmlHydrogenase-1 small chainP69739MBHS_ECOLIhyaAhttp://ecmdb.ca/proteins/P69739.xmlHydrogenase-2 small chainP69741MBHT_ECOLIhybOhttp://ecmdb.ca/proteins/P69741.xmlHydrogenase-4 component JP77453HYFJ_ECOLIhyfJhttp://ecmdb.ca/proteins/P77453.xmlHydrogenase-4 component DP77416HYFD_ECOLIhyfDhttp://ecmdb.ca/proteins/P77416.xmlHydrogenase-4 component GP77329HYFG_ECOLIhyfGhttp://ecmdb.ca/proteins/P77329.xmlProbable Ni/Fe-hydrogenase 1 B-type cytochrome subunitP0AAM1CYBH_ECOLIhyaChttp://ecmdb.ca/proteins/P0AAM1.xmlHydrogenase-4 component FP77437HYFF_ECOLIhyfFhttp://ecmdb.ca/proteins/P77437.xmlHydrogenase-2 operon protein hybAP0AAJ8HYBA_ECOLIhybAhttp://ecmdb.ca/proteins/P0AAJ8.xmlHydrogenase-4 component EP0AEW1HYFE_ECOLIhyfEhttp://ecmdb.ca/proteins/P0AEW1.xmlProbable Ni/Fe-hydrogenase 2 b-type cytochrome subunitP37180HYBB_ECOLIhybBhttp://ecmdb.ca/proteins/P37180.xmlHydrogenase-4 component CP77858HYFC_ECOLIhyfChttp://ecmdb.ca/proteins/P77858.xmlHydrogenase-4 component IP77668HYFI_ECOLIhyfIhttp://ecmdb.ca/proteins/P77668.xmlHydrogenase-4 component BP23482HYFB_ECOLIhyfBhttp://ecmdb.ca/proteins/P23482.xmlFormate hydrogenlyase subunit 3P16429HYCC_ECOLIhycChttp://ecmdb.ca/proteins/P16429.xmlHydrogenase-4 component HP77423HYFH_ECOLIhyfHhttp://ecmdb.ca/proteins/P77423.xmlHydrogenase-4 component AP23481HYFA_ECOLIhyfAhttp://ecmdb.ca/proteins/P23481.xmlFormate hydrogenlyase subunit 4P16430HYCD_ECOLIhycDhttp://ecmdb.ca/proteins/P16430.xmlGalactose-proton symporterP0AEP1GALP_ECOLIgalPhttp://ecmdb.ca/proteins/P0AEP1.xmlMelibiose carrier proteinP02921MELB_ECOLImelBhttp://ecmdb.ca/proteins/P02921.xmlH(+)/Cl(-) exchange transporter ClcAB1XD25CLCA_ECODHclcAhttp://ecmdb.ca/proteins/B1XD25.xmlThreonine/serine transporter tdcCC4ZR30TDCC_ECOBWtdcChttp://ecmdb.ca/proteins/C4ZR30.xmlH(+)/Cl(-) exchange transporter ClcAC4ZRP8CLCA_ECOBWclcAhttp://ecmdb.ca/proteins/C4ZRP8.xmlThreonine/serine transporter tdcCP0AAD8TDCC_ECOLItdcChttp://ecmdb.ca/proteins/P0AAD8.xmlArabinose-proton symporterP0AE24ARAE_ECOLIaraEhttp://ecmdb.ca/proteins/P0AE24.xmlD-xylose-proton symporterP0AGF4XYLE_ECOLIxylEhttp://ecmdb.ca/proteins/P0AGF4.xmlProline/betaine transporterP0C0L7PROP_ECOLIproPhttp://ecmdb.ca/proteins/P0C0L7.xmlH(+)/Cl(-) exchange transporter ClcAP37019CLCA_ECOLIclcAhttp://ecmdb.ca/proteins/P37019.xmlOuter membrane protein NP77747OMPN_ECOLIompNhttp://ecmdb.ca/proteins/P77747.xmlOuter membrane pore protein EP02932PHOE_ECOLIphoEhttp://ecmdb.ca/proteins/P02932.xmlOuter membrane protein FP02931OMPF_ECOLIompFhttp://ecmdb.ca/proteins/P02931.xmlOuter membrane protein CP06996OMPC_ECOLIompChttp://ecmdb.ca/proteins/P06996.xml2 Hydrogen ion + Hydrogen (gas) + Ubiquinone-8 > Ubiquinol-8 +2 Hydrogen ion2-Demethylmenaquinone 8 + 2 Hydrogen ion + Hydrogen (gas) > 2-Demethylmenaquinol 8 +2 Hydrogen ion2 Hydrogen ion + Hydrogen (gas) + Menaquinone 8 > Menaquinol 8 +2 Hydrogen ionFormic acid + Hydrogen ion > Carbon dioxide + Hydrogen (gas)FHLMULTI-RXNWater + Phosphonate > Hydrogen (gas) + PhosphateHydrogen ion + Formic acid > Carbon dioxide + Hydrogen (gas)FHLMULTI-RXNHydrogen ion > Hydrogen (gas)RXN0-3283a menaquinone + Hydrogen ion + Hydrogen (gas) > a menaquinol + Hydrogen ionRXN0-5256Hydrogen (gas) + A > AH(2)Hydrogen (gas) + Acceptor <> Reduced acceptorR07182