PDBsum entry: 1g72

Oxidoreductase

PDB id: 1g72

Contents

Protein chains

571 a.a. *

57 a.a. *

Ligands

PQQ ×2

Metals

_CA ×2

Waters ×614

* Residue conservation analysis

PDB id:

1g72

Name:

Oxidoreductase

Title:

Catalytic mechanism of quinoprotein methanol dehydrogenase: theoretical and x-ray crystallographic investigation

Structure:

Methanol dehydrogenase heavy subunit. Chain: a, c. Synonym: mdh large alpha subunit. Methanol dehydrogenase light subunit. Chain: b, d. Synonym: mdh small alpha subunit. Ec: 1.1.99.8

Source:

Methylophilus methylotrophus. Organism_taxid: 2327. Strain: w3a1. Strain: w3a1

Biol. unit:

Tetramer (from PQS)

Resolution:

1.90Å R-factor: 0.161 R-free: 0.190

Authors:

Y.Zheng,Z.Xia,Z.Chen,T.C.Bruice,F.S.Mathews

Key ref:

Y.J.Zheng et al. (2001). Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation. Proc Natl Acad Sci U S A, 98, 432-434. PubMed id: 11149955 DOI: 10.1073/pnas.021547498

Date:

08-Nov-00 Release date: 24-Jan-01

Supersedes:

1b2n

Protein chains

P38539  (DHM1_METME) -  Methanol dehydrogenase [cytochrome c] subunit 1

Seq: 573 a.a.

Struc: 571 a.a.

Protein chains

P38540  (DHM2_METME) -  Methanol dehydrogenase [cytochrome c] subunit 2

Seq: 91 a.a.

Struc: 57 a.a.

Enzyme reactions

• Enzyme class: Chains A, B, C, D: E.C.1.1.2.7 - Methanol dehydrogenase (cytochrome c).
• Reaction: A primary alcohol + 2 cytochrome c(L) = an aldehyde + 2 reduced cytochrome c(L)
• Cofactor: Pyrroloquinoline quinone

Pyrroloquinoline quinone (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 (3 terms)
• Biological process: oxidation-reduction process (3 terms)
• Biochemical function: oxidoreductase activity (5 terms)

reference

DOI no: 10.1073/pnas.021547498

Proc Natl Acad Sci U S A 98:432-434 (2001)

PubMed id: 11149955

Catalytic mechanism of quinoprotein methanol dehydrogenase: A theoretical and x-ray crystallographic investigation.

Y.J.Zheng, Xia Zx, Chen Zw, F.S.Mathews, T.C.Bruice.

ABSTRACT

The catalytic mechanism of the reductive half reaction of the quinoprotein methanol dehydrogenase (MDH) is believed to proceed either through a hemiketal intermediate or by direct transfer of a hydride ion from the substrate methyl group to the cofactor, pyrroloquinoline quinone (PQQ). A crystal structure of the enzyme-substrate complex of a similar quinoprotein, glucose dehydrogenase, has recently been reported that strongly favors the hydride transfer mechanism in that enzyme. A theoretical analysis and an improved refinement of the 1.9-A resolution crystal structure of MDH from Methylophilus methylotrophus W3A1 in the presence of methanol, reported earlier, indicates that the observed tetrahedral configuration of the C-5 atom of PQQ in that study represents the C-5-reduced form of the cofactor and lends support for a hydride transfer mechanism for MDH.

Selected figure(s)

Figure 1.
Fig. 1. (A) Chemical structure of PQQ with the numbering of the ring atoms indicated. (B) Addition-elimination mechanism for oxidation of methanol by PQQ in methanol dehydrogenase involving base catalysis by Asp297. (C) Hydride transfer mechanism for methanol oxidation involving a C-5-reduced intermediate of PQQ and base catalysis by Asp297.

Figure 3.
Fig. 3. Environment of the water molecule hydrogen bonded to Asp297 and C-5 of PQQ. Electrostatic and hydrogen bonding interactions are indicated by dotted lines, and van der Waals interactions by dashed lines with distances in Å. This diagram was prepared by using the program MOLSCRIPT (23).

Figures were selected by an automated process.