PDBsum entry: 1h4j

Oxidoreductase

PDB id: 1h4j

Contents

Protein chains

595 a.a. *

72 a.a. *

Ligands

PQQ ×4

Metals

_CA ×4

* Residue conservation analysis

PDB id:

1h4j

Name:

Oxidoreductase

Title:

Methylobacterium extorquens methanol dehydrogenase d303e mutant

Structure:

Methanol dehydrogenase subunit 1. Chain: a, c, e, g. Synonym: mdh large, alpha subunit, medh. Mutation: yes. Methanol dehydrogenase subunit 2. Chain: b, d, f, h. 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:

3.00Å R-factor: 0.187 R-free: 0.217

Authors:

F.Mohammed,R.Gill,D.Thompson,J.B.Cooper,S.P.Wood, P.R.Afolabi,C.Anthony

Key ref:

P.R.Afolabi et al. (2001). Site-directed mutagenesis and X-ray crystallography of the PQQ-containing quinoprotein methanol dehydrogenase and its electron acceptor, cytochrome c(L). Biochemistry, 40, 9799-9809. PubMed id: 11502173 DOI: 10.1021/bi002932l

Date:

11-May-01 Release date: 23-Aug-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: 72 a.a.

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

Enzyme reactions

• Enzyme class: Chains A, B, C, D, E, F, G, H: 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: 10.1021/bi002932l

Biochemistry 40:9799-9809 (2001)

PubMed id: 11502173

Site-directed mutagenesis and X-ray crystallography of the PQQ-containing quinoprotein methanol dehydrogenase and its electron acceptor, cytochrome c(L).

P.R.Afolabi, F.Mohammed, K.Amaratunga, O.Majekodunmi, S.L.Dales, R.Gill, D.Thompson, J.B.Cooper, S.P.Wood, P.M.Goodwin, C.Anthony.

ABSTRACT

Two proteins specifically involved in methanol oxidation in the methylotrophic bacterium Methylobacterium extorquens have been modified by site-directed mutagenesis. Mutation of the proposed active site base (Asp303) to glutamate in methanol dehydrogenase (MDH) gave an active enzyme (D303E-MDH) with a greatly reduced affinity for substrate and with a lower activation energy. Results of kinetic and deuterium isotope studies showed that the essential mechanism in the mutant protein was unchanged, and that the step requiring activation by ammonia remained rate limiting. No spectrally detectable intermediates could be observed during the reaction. The X-ray structure, determined to 3 A resolution, of D303E-MDH showed that the position and coordination geometry of the Ca2+ ion in the active site was altered; the larger Glu303 side chain was coordinated to the Ca2+ ion and also hydrogen bonded to the O5 atom of pyrroloquinoline quinone (PQQ). The properties and structure of the D303E-MDH are consistent with the previous proposal that the reaction in MDH is initiated by proton abstraction involving Asp303, and that the mechanism involves a direct hydride transfer reaction. Mutation of the two adjacent cysteine residues that make up the novel disulfide ring in the active site of MDH led to an inactive enzyme, confirming the essential role of this remarkable ring structure. Mutations of cytochrome c(L), which is the electron acceptor from MDH was used to identify Met109 as the sixth ligand to the heme.