1QV9

Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: A methanogenic enzyme with an unusual quarternary structure

Summary for 1QV9

• Entry DOI: 10.2210/pdb1qv9/pdb
• Descriptor: F420-dependent methylenetetrahydromethanopterin dehydrogenase, MAGNESIUM ION (3 entities in total)
• Functional Keywords: monomer: alpha/beta domain, helix bundle; trimer of dimers, oxidoreductase
• Biological source: Methanopyrus kandleri
• Total number of polymer chains: 3
• Total formula weight: 96736.52

Authors

Hagemeier, C.H.,Shima, S.,Thauer, R.K.,Bourenkov, G.,Bartunik, H.D.,Ermler, U. (deposition date: 2003-08-27, release date: 2003-11-11, Last modification date: 2024-11-20)

Primary citation

Hagemeier, C.H.,Shima, S.,Thauer, R.K.,Bourenkov, G.,Bartunik, H.D.,Ermler, U.
Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: a methanogenic enzyme with an unusual quarternary structure
J.Mol.Biol., 332:1047-1057, 2003

PubMed Abstract: The fourth reaction step of CO(2)-reduction to methane in methanogenic archaea is catalyzed by coenzyme F(420)-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd). We have structurally characterized this enzyme in the selenomethionine-labelled form from the hyperthermophilic methanogenic archaeon Methanopyrus kandleri at 1.54A resolution using the single wavelength anomalous dispersion method for phase determination. Mtd was found to be a homohexameric protein complex that is organized as a trimer of dimers. The fold of the individual subunits is composed of two domains: a larger alpha,beta domain and a smaller helix bundle domain with a short C-terminal beta-sheet segment. In the homohexamer the alpha,beta domains are positioned at the outside of the enzyme, whereas, the helix bundle domains assemble towards the inside to form an unusual quarternary structure with a 12-helix bundle around a 3-fold axis. No structural similarities are detectable to other enzymes with F(420) and/or substituted tetrahydropterins as substrates. The substrate binding sites of F(420) and methylenetetrahydromethanopterin are most likely embedded into a crevice between the domains of one subunit, their isoalloxazine and tetrahydropterin rings being placed inside a pocket formed by this crevice and a loop segment of the adjacent monomer of the dimer. Mtd revealed the highest stability at low salt concentrations of all structurally characterized enzymes from M.kandleri. This finding might be due to the compact quaternary structure that buries 36% of the monomer surface and to the large number of ion pairs.

PubMed: 14499608
DOI: 10.1016/S0022-2836(03)00949-5

Experimental method

X-RAY DIFFRACTION (1.54 Å)