PDBsum entry: 1h4i

Dehydrogenase

PDB id: 1h4i

Contents

Protein chains

595 a.a. *

73 a.a. *

Ligands

PQQ ×2

Metals

_CA ×2

* Residue conservation analysis

PDB id:

1h4i

Name:

Dehydrogenase

Title:

Methylobacterium extorquens methanol dehydrogenase

Structure:

Methanol dehydrogenase subunit 1. Chain: a, c. Synonym: mdh large, alpha subunit, medh. Methanol dehydrogenase subunit 2. Chain: b, d. Synonym: mdh small, beta subunit, medh. Other_details: pyrrolo-quinoline quinone prosthetic group with active site calcium ions

Source:

Methylobacterium extorquens. Organism_taxid: 408. Organism_taxid: 408

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.94Å R-factor: 0.198 R-free: 0.229

Authors:

M.Ghosh,C.Anthony,K.Harlos,M.G.Goodwin,C.Blake

Key ref:

M.Ghosh et al. (1995). The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A. Structure, 3, 177-187. PubMed id: 7735834 DOI: 10.1016/S0969-2126(01)00148-4

Date:

11-May-01 Release date: 14-Jun-01

Protein chains

P16027  (DHM1_METEA) -  Methanol dehydrogenase [cytochrome c] subunit 1

Seq: 626 a.a.

Struc: 595 a.a.

Protein chains

P14775  (DHM2_METEA) -  Methanol dehydrogenase [cytochrome c] subunit 2

Seq: 96 a.a.

Struc: 73 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.1.1.99.8 - Transferred entry: 1.1.2.7 and 1.1.2.8.
• Reaction: A primary alcohol + acceptor = an aldehyde + reduced acceptor
• Cofactor: PQQ

(Bound ligand (Het Group name = PQQ) corresponds exactly)

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

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (4 terms)
• Biological process: oxidation reduction (3 terms)
• Biochemical function: oxidoreductase activity (6 terms)

reference

DOI no: 10.1016/S0969-2126(01)00148-4

Structure 3:177-187 (1995)

PubMed id: 7735834

The refined structure of the quinoprotein methanol dehydrogenase from Methylobacterium extorquens at 1.94 A.

M.Ghosh, C.Anthony, K.Harlos, M.G.Goodwin, C.Blake.

ABSTRACT

BACKGROUND: Methanol dehydrogenase (MDH) is a bacterial periplasmic quinoprotein; it has pyrrolo-quinoline quinone (PQQ) as its prosthetic group, requires Ca2+ for activity and uses cytochrome cL as its electron acceptor. Low-resolution structures of MDH have already been determined. RESULTS: The structure of the alpha 2 beta 2 tetramer of MDH from Methylobacterium extorquens has now been determined at 1.94 A with an R-factor of 19.85%. CONCLUSIONS: The alpha-subunit of MDH has an eight-fold radial symmetry, with its eight beta-sheets stabilized by a novel tryptophan docking motif. The PQQ in the active site is held in place by a coplanar tryptophan and by a novel disulphide ring formed between adjacent cysteines which are bonded by an unusual non-planar trans peptide bond. One of the carbonyl oxygens of PQQ is bonded to the Ca2+, probably facilitating attack on the substrate, and the other carbonyl oxygen is out of the plane of the ring, confirming the presence of the predicted free-radical semiquinone form of the prosthetic group.

Selected figure(s)

Figure 6.
Figure 6. A stereo drawing of the MDH tetramer showing the girdle of tryptophan docking motifs around each α-subunit. The molecular two-fold axis is inclined at about 45° to demonstrate the circular, planar nature of the girdle. Figure 6. A stereo drawing of the MDH tetramer showing the girdle of tryptophan docking motifs around each α-subunit. The molecular two-fold axis is inclined at about 45° to demonstrate the circular, planar nature of the girdle.

Figure 7.
Figure 7. A stereo drawing of the electron density around the Cys103–Cys104 disulphide bridge and the interpretation of the feature with a non-planar linking peptide bond, giving a novel eight-membered ring structure. Figure 7. A stereo drawing of the electron density around the Cys103–Cys104 disulphide bridge and the interpretation of the feature with a non-planar linking peptide bond, giving a novel eight-membered ring structure.

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 177-187) copyright 1995.

Figures were selected by an automated process.