Literature summary for 1.8.7.3 extracted from

Watanabe, T.; Pfeil-Gardiner, O.; Kahnt, J.; Koch, J.; Shima, S.; Murphy, B.
Three-megadalton complex of methanogenic electron-bifurcating and CO2-fixing enzymes (2021), Science, 373, 1151-1156 .

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified dimeric Fdh-Hdr-Fmd, X-ray diffraction structure analysis at 2.6 A resolution and mapping of the HdrABC dimeric core (excluding N- and C-terminal domains of HdrA), symmetry expansion and focused classifications and refinements give subregions at 3.0-3.6 A resolution	Methanospirillum hungatei

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Fe2+	in (4Fe-4S)clusters	Methanospirillum hungatei

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
2 reduced ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB + 2 H+	Methanospirillum hungatei	-	2 oxidized ferredoxin [iron-sulfur] cluster + CoB + CoM	-	?

Organism

Organism	UniProt	Comment	Textmining
Methanospirillum hungatei	Q2FKZ1	-	-

Purification (Commentary)

Purification (Comment)	Organism
purification of a massive (megadalton) complex of the electron-bifurcating Fdh-Hdr together with the CO2-reducing Fmd (Fdh-Hdr-Fmd hexamer), as well as of dimeric Fdh-Hdr-Fmd and Fdh-Hdr subcomplexes by anion exchange chromatography and gel filtration. Mass spectrometry reveals that the Fdh-Hdr-Fmd complex elutes from gel filtration primarily as a 1-MDa dimer of subunits FdhAB-MvhD-HdrABCFmdABCDFG. The Fdh-Hdr complexes are isolated as two oligomeric states, which contain FdhAB-MvhD-HdrABCFmdF. Two of five isoenzymes of FdhA and are detected in all complexes	Methanospirillum hungatei

Purification (Comment)

Organism

purification of a massive (megadalton) complex of the electron-bifurcating Fdh-Hdr together with the CO2-reducing Fmd (Fdh-Hdr-Fmd hexamer), as well as of dimeric Fdh-Hdr-Fmd and Fdh-Hdr subcomplexes by anion exchange chromatography and gel filtration. Mass spectrometry reveals that the Fdh-Hdr-Fmd complex elutes from gel filtration primarily as a 1-MDa dimer of subunits FdhAB-MvhD-HdrABCFmdABCDFG. The Fdh-Hdr complexes are isolated as two oligomeric states, which contain FdhAB-MvhD-HdrABCFmdF. Two of five isoenzymes of FdhA and are detected in all complexes

Methanospirillum hungatei

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
2 reduced ferredoxin [iron-sulfur] cluster + CoM-S-S-CoB + 2 H+	-	Methanospirillum hungatei	2 oxidized ferredoxin [iron-sulfur] cluster + CoB + CoM	-	?

Subunits

Subunits	Comment	Organism
More	three-dimensional map and model of the dimeric Fdh-Hdr-Fmd complex, its active sites, and Fe-S cluster relay. The structure of the D3-hexameric complex is made by threefold repetition of the dimeric structure, and contains dimeric organization of Hdr and Fmd subunits. Mass spectrometry reveals that the Fdh-Hdr-Fmd complex elutes from gel filtration primarily as a 1-MDa dimer of subunits FdhAB-MvhD-HdrABCFmdABCDFG. The Fdh-Hdr complexes are isolated as two oligomeric states, which contain FdhAB-MvhD-HdrABCFmdF. Two of five isoenzymes of FdhA and are detected in all complexes	Methanospirillum hungatei

Synonyms

Synonyms	Comment	Organism
CoB-CoM heterodisulfide reductase iron-sulfur subunit A	-	Methanospirillum hungatei
HDR	-	Methanospirillum hungatei
HdrABC	-	Methanospirillum hungatei
heterodisulfide reductase	-	Methanospirillum hungatei
Mhun_1838	-	Methanospirillum hungatei

Cofactor

Cofactor	Comment	Organism
FAD	required for activity. Conformational changes within the HdrA subunit provide a conformationally gated pathway for electrons to and from the bifurcating flavin adenine dinucleotide (FAD)	Methanospirillum hungatei
Ferredoxin	-	Methanospirillum hungatei
additional information	the enzyme contains (4Fe-4S)clusters	Methanospirillum hungatei

General Information

General Information	Comment	Organism
evolution	conservation of Hdr and Fmd structures suggests that the complex of both is common among hydrogenotrophic methanogens	Methanospirillum hungatei
metabolism	the first reaction of the methanogenic pathway from carbon dioxide (CO2) is the reduction and condensation of CO2 to formyl-methanofuran, catalyzed by formyl-methanofuran dehydrogenase (Fmd, EC 1.12.7.2). Strongly reducing electrons for this reaction are generated by heterodisulfide reductase (Hdr, EC 1.8.7.3) in complex with hydrogenase or formate dehydrogenase (Fdh) using a flavin-based electron-bifurcation mechanism	Methanospirillum hungatei
additional information	enzymological and structural characterizations of Fdh-Hdr-Fmd complexes from Methanospirillum hungatei. The complexes catalyze the reaction using electrons from formate and the reduced form of the electron carrier F420. Conformational changes in HdrA mediate electron bifurcation, and polyferredoxin FmdF directly transfers electrons to the CO2 reduction site, as evidenced by methanofuran-dependent flavin-based electron bifurcation even without free ferredoxin, a diffusible electron carrier between Hdr and Fmd. Conformational changes within the HdrA subunit provide a conformationally gated pathway for electrons to and from the bifurcating flavin adenine dinucleotide (FAD). The dimeric Fdh- Hdr-Fmd structure reveals that FdhAB and HdrABC are connected via MvhD and that a polyferredoxin FmdF bridges HdrABC and FmdABCDG. Tertiary and quartenary enzyme complex structures and structure-function analysis, detailed overview	Methanospirillum hungatei
physiological function	in the hydrogenotrophic methanogenic pathway, CO2 is reduced and then condensed to a C1-carrier methanofuran to form formyl-methanofuran. These reactions are catalyzed by the molybdenum-containing formyl-methanofuran dehydrogenase (EC 1.12.7.2), FmdABCDFG, or its tungsten isoform, FwdABCDFG. Electrons for CO2 reduction are provided by methyl viologen-reducing hydrogenase (MvhAG, EC 1.8.98.1) or formate dehydrogenase (FdhAB, EC 1.8.98.6) in complex with heterodisulfide reductase (HdrABC), which carries out flavin-based electron bifurcation (FBEB). In this process, the energy in a pair of electrons is split, giving rise to a strongly reducing electron for CO2 fixation and a weakly reducing electron for reduction of the heterodisulfide of coenzyme M and coenzyme B (CoM-S-S-CoB), a co-oxidant that is regenerated by the methane formation reaction. The electron transfer chain leads from formate via molybdopterin in FdhA to the FBEB-catalyzing HdrA. FdhB contains a partially solvent-exposed FAD molecule that forms a likely F420-binding site, which shows a fold similar to that of the FAD-containing site of F420-reducing hydrogenase (Frh). The electron transfer chains from FdhB FAD and the FdhA active site converge at an unpredicted [4Fe-4S] cluster with ligation from one histidine and three cysteine residues, and the [4Fe-4S] clusters in FdhAB form a conductive pathway with distances below 14 A	Methanospirillum hungatei