PDBsum entry: 1w6s

Oxidoreductase

PDB id: 1w6s

Contents

Protein chains

596 a.a. *

73 a.a. *

Ligands

PQQ ×2

GOL ×3

Metals

_CA ×2

Waters ×1437

* Residue conservation analysis

PDB id:

1w6s

Name:

Oxidoreductase

Title:

The high resolution structure of methanol dehydrogenase from methylobacterium extorquens

Structure:

Methanol dehydrogenase subunit 1. Chain: a, c. Synonym: mdh large subunit, medh. Methanol dehydrogenase subunit 2. Chain: b, d. Synonym: mdh small subunit, medh. Ec: 1.1.99.8

Source:

Methylobacterium extorquens. Organism_taxid: 408. Organism_taxid: 408

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.2Å R-factor: 0.152 R-free: 0.176

Authors:

P.A.Williams,L.Coates,F.Mohammed,R.Gill,P.T.Erskine, S.P.Wood,C.Anthony,J.B.Cooper

Key ref:

P.A.Williams et al. (2005). The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens. Acta Crystallogr D Biol Crystallogr, 61, 75-79. PubMed id: 15608378 DOI: 10.1107/S0907444904026964

Date:

23-Aug-04 Release date: 21-Dec-04

Protein chains

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

Seq: 626 a.a.

Struc: 596 a.a.*

Protein chains

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

Seq: 96 a.a.

Struc: 73 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

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: 10.1107/S0907444904026964

Acta Crystallogr D Biol Crystallogr 61:75-79 (2005)

PubMed id: 15608378

The atomic resolution structure of methanol dehydrogenase from Methylobacterium extorquens.

P.A.Williams, L.Coates, F.Mohammed, R.Gill, P.T.Erskine, A.Coker, S.P.Wood, C.Anthony, J.B.Cooper.

ABSTRACT

The crystal structure of methanol dehydrogenase (MDH) from Methylobacterium extorquens has been refined without stereochemical restraints at a resolution of 1.2 A. The high-resolution data have defined the conformation of the tricyclic pyrroloquinoline quinone (PQQ) cofactor ring as entirely planar. The detailed definition of the active-site geometry has shown many features that are similar to the quinohaemo-protein alcohol dehydrogenases from Comamonas testosteroni and Pseudomonas putida, both of which possess MDH-like and cytochrome c-like domains. Conserved features between the two types of PQQ-containing enzyme suggest a common pathway for electron transfer between MDH and its physiological electron acceptor cytochrome cL. A pathway for proton transfer from the active site to the bulk solvent is also suggested.

Selected figure(s)

Figure 2.
Figure 2 The equatorial interactions of PQQ in the active site and the dative bonds that coordinate the calcium. The lengths of the bonds to the Ca^2+ ion are all between 2.4 and 2.8 Å. The orthoquinone group is formed by the central six-membered ring with two O-atom substituents. The vicinal disulfide bond formed by cysteines 103 and 104, which packs against the PQQ ring, has been omitted for clarity.

Figure 3.
Figure 3 The interactions made by the active-site Ca^2+ ion. The length of the interaction between Asn261 and the Ca^2+ ion is 3.18 Å, which is too long to be considered a coordinated bond. The 1.2 Å resolution 2F[o] - F[c] map contoured at the 1.0 level is shown in grey/blue lines.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2005, 61, 75-79) copyright 2005.

Figures were selected by an automated process.