PDBsum entry 6tge

Oxidoreductase

PDB id: 6tge

Contents

Protein chains

(+ 18 more) 287 a.a.

Ligands

NAP ×24

H4M ×24

SO4 ×8

Waters ×7743

PDB id:

6tge

Name:

Oxidoreductase

Title:

NADP dependent methylene-tetrahydromethanopterin dehydrogenase-NADP+- methenyl-h4mpt+ complex

Structure:

Bifunctional NADP-dependent methylenetetrahydromethanopterin dehydrogenase/methylenetetrahydrofolate dehydrogenase. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n, o, p, q, r, s, t, u, v, w, x. Synonym: NADP-dependent methylenetetrahydromethanopterin/methylenetetrahydrofolat e dehydrogenase. Engineered: yes

Source:

Methylorubrum extorquens. Organism_taxid: 408. Gene: mtda, bv511_24355, tk0001_4179. Expressed in: escherichia coli 'bl21-gold(de3)plyss ag'. Expression_system_taxid: 866768

Resolution:

1.50Å R-factor: 0.187 R-free: 0.216

Authors:

U.Ermler,S.Shima

Key ref:

G.Huang et al. (2020). The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase. J Mol Biol, 432, 2042-2054. PubMed id: 32061937 DOI: 10.1016/j.jmb.2020.01.042

Date:

15-Nov-19 Release date: 26-Feb-20

Protein chains

P55818  (MTDA_METEA) -  Bifunctional protein MdtA from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)

Seq: 288 a.a.

Struc: 287 a.a.

Enzyme reactions

• Enzyme class 1: E.C.1.5.1.- - ?????
• Enzyme class 2: E.C.1.5.1.5 - methylenetetrahydrofolate dehydrogenase (NADP(+)).

Pathway:

• Reaction: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP⁺ = (6R)-5,10- methenyltetrahydrofolate + NADPH

(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NAP) corresponds exactly) = (6R)-5,10- methenyltetrahydrofolate + NADPH

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.jmb.2020.01.042

J Mol Biol 432:2042-2054 (2020)

PubMed id: 32061937

The Hydride Transfer Process in NADP-dependent Methylene-tetrahydromethanopterin Dehydrogenase.

G.Huang, T.Wagner, U.Demmer, E.Warkentin, U.Ermler, S.Shima.

ABSTRACT

NADP-dependent methylene-tetrahydromethanopterin (methylene-H₄MPT) dehydrogenase (MtdA) catalyzes the reversible dehydrogenation of methylene-H₄MPT to form methenyl-H₄MPT⁺ by using NADP⁺ as a 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° rotation of the NADP, relative to the pterin domain. The 1.08 Å 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 Å structure of MtdA in complex with the nonreactive NADP⁺ and methenyl-H₄MPT⁺ revealed an extremely short distance between nicotinamide-C4 and imidazoline-C14a of 2.5 Å, 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.