PDBsum entry: 2d0v

Oxidoreductase

PDB id: 2d0v

Contents

Protein chains

597 a.a. *

70 a.a. *

Ligands

PQQ ×3

Metals

_CA ×3

Waters ×727

* Residue conservation analysis

PDB id:

2d0v

Name:

Oxidoreductase

Title:

Crystal structure of methanol dehydrogenase from hyphomicrobium denitrificans

Structure:

Methanol dehydrogenase large subunit. Chain: a, d, i. Methanol dehydrogenase small subunit. Chain: b, e, j. Ec: 1.1.99.8

Source:

Hyphomicrobium denitrificans. Organism_taxid: 53399. Strain: a3151. Strain: a3151

Biol. unit:

Tetramer (from PDB file)

Resolution:

2.49Å R-factor: 0.159 R-free: 0.247

Authors:

M.Nojiri,D.Hira,K.Yamaguchi,S.Suzuki

Key ref:

M.Nojiri et al. (2006). Crystal Structures of Cytochrome c(L) and Methanol Dehydrogenase from Hyphomicrobium denitrificans: Structural and Mechanistic Insights into Interactions between the Two Proteins(,). Biochemistry, 45, 3481-3492. PubMed id: 16533029 DOI: 10.1021/bi051877j

Date:

09-Aug-05 Release date: 09-Aug-06

Protein chains

Q4AE26  (Q4AE26_9RHIZ) -  Methanol dehydrogenase large subunit (Fragment)

Seq: 597 a.a.

Struc: 597 a.a.

Protein chains

Q4AE23  (Q4AE23_9RHIZ) -  Methanol dehydrogenase small subunit

Seq: 101 a.a.

Struc: 70 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (2 terms)
• Biological process: oxidation reduction (2 terms)
• Biochemical function: oxidoreductase activity, acting on CH-OH group of donors (3 terms)

DOI no: 10.1021/bi051877j

Biochemistry 45:3481-3492 (2006)

PubMed id: 16533029

Crystal Structures of Cytochrome c(L) and Methanol Dehydrogenase from Hyphomicrobium denitrificans: Structural and Mechanistic Insights into Interactions between the Two Proteins(,).

M.Nojiri, D.Hira, K.Yamaguchi, T.Okajima, K.Tanizawa, S.Suzuki.

ABSTRACT

Methanol dehydrogenase (Hd-MDH) and its physiological electron acceptor, cytochrome c(L) (Hd-Cyt c(L)), isolated from a methylotrophic denitrifying bacterium, Hyphomicrobium denitrificans A3151, have been kinetically and structurally characterized; the X-ray structures of Hd-MDH and Hd-Cyt c(L) have been determined using molecular replacement at 2.5 and 2.0 A resolution, respectively. To explain the mechanism for electron transfer between these proteins, the dependence of MDH activity on the concentration of Hd-Cyt c(L) has been investigated at pH 4.5-7.0. The Michaelis constant for Hd-Cyt c(L) shows the smallest value ( approximately 0.3 muM) at pH 5.5. The pseudo-first-order rate constant (k(obs)) of the reduction of Hd-Cyt c(L) exhibits a hyperbolic concentration dependence of Hd-MDH at pH 5.5, although k(obs) linearly increases at pH 6.5. These findings indicate formation of a transient complex between these proteins during an electron transfer event. Hd-MDH (148 kDa) is a large tetrameric protein with an alpha(2)beta(2) subunit composition, showing a high degree of structural similarity with other MDHs. Hd-Cyt c(L) (19 kDa) exhibiting the alpha-band at 550.7 nm has a unique C-terminal region involving a disulfide bond between Cys47 and Cys165. Moreover, there is a pair of Hd-Cyt c(L) monomers related with a pseudo-2-fold axis of symmetry in the asymmetric unit, and the two monomers tightly interact with each other through three hydrogen bonds. This configuration is the first example in the studies of cytochrome c as the physiological electron acceptor for MDH. The docking simulation between the coupled Hd-Cyt c(L) molecules and the heterotetrameric Hd-MDH molecule has been carried out.