6yk9 | pdb_00006yk9

[Fe]-hydrogenase from Methanolacinia paynteri with bound guanylylpyridinol at 1.7-A resolution

spinqualitylabelsall models 6yk9, resolution 1.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.7Å Ligands: 5GP, EDO, FEG, GLY, GMP Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed NADP-dependent methylene-tetrahydromethanopterin (methylene-H4MPT) dehydrogenase (MtdA) catalyzes the reversible dehydrogenation of methylene-H4MPT to form methenyl-H4MPT(+) by using NADP(+) as hydride acceptor. This hydride transfer reaction is involved in the oxidative metabolism from formaldehyde to CO2 in methylotrophic and methanotrophic bacteria. Here, we report on the crystal structures of the ternary MtdA-substrate complexes from Methylorubrum extorquens AM1 obtained in open and closed forms. Their conversion is accomplished by opening/closing the active site cleft via a 15 degrees rotation of the NADP- relative to the pterin-domain. The 1.08-A structure of the closed and active enzyme- NADP(+)-methylene-H4MPT complex allows a detailed geometric analysis of the bulky substrates and a precise prediction of the hydride trajectory. Upon domain closure, the bulky substrate rings become compressed resulting in a tilt of the imidazolidine group of methylene-H4MPT that optimizes the geometry for hydride transfer. An additional 1.5-A structure of MtdA in complex with the non-reactive NADP(+) and methenyl-H4MPT(+) revealed an extremely short distance between nicotinamide-C4 and imidazoline-C14a of 2.5 A, which demonstrates the strong pressure imposed. The pterin-imidazolidine-phenyl butterfly angle of methylene-H4MPT bound to MtdA is smaller than that in the enzyme-free state but is similar to that in H2- and F420-dependent methylene-H4MPT dehydrogenases. The concept of compression-driven hydride-transfer including quantum-mechanical hydrogen-tunneling effects, which are established for flavin- and NADP-dependent enzymes, can be expanded to hydride-transferring H4MPT-dependent enzymes. The hydride transfer process in NADP dependent methylene-tetrahydromethanopterin dehydrogenase.,Huang G, Wagner T, Demmer U, Warkentin E, Ermler U, Shima S J Mol Biol. 2020 Feb 13. pii: S0022-2836(20)30108-X. doi:, 10.1016/j.jmb.2020.01.042. PMID:32061937 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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