PDBsum entry: 1lrw

Oxidoreductase

PDB id: 1lrw

Contents

Protein chains

600 a.a. *

83 a.a. *

Ligands

PQQ ×2

Metals

_CA ×2

Waters ×403

* Residue conservation analysis

PDB id:

1lrw

Name:

Oxidoreductase

Title:

Crystal structure of methanol dehydrogenase from p. Denitrificans

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. Ec: 1.1.99.8

Source:

Paracoccus denitrificans. Organism_taxid: 266. Organism_taxid: 266

Biol. unit:

Tetramer (from PQS)

Resolution:

2.50Å R-factor: 0.179 R-free: 0.238

Authors:

Z.-X.Xia,W.-W.Dai,Y.-N.He,S.A.White,F.S.Mathews,V.L.Davidson

Key ref:

Z.X.Xia et al. (2003). X-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i. J Biol Inorg Chem, 8, 843-854. PubMed id: 14505072 DOI: 10.1007/s00775-003-0485-0

Date:

16-May-02 Release date: 12-Aug-03

Protein chains

P12293  (DHM1_PARDE) -  Methanol dehydrogenase [cytochrome c] subunit 1

Seq: 631 a.a.

Struc: 600 a.a.*

Protein chains

P29898  (DHM2_PARDE) -  Methanol dehydrogenase [cytochrome c] subunit 2

Seq: 103 a.a.

Struc: 83 a.a.

* PDB and UniProt seqs differ at 9 residue positions (black crosses)

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 (3 terms)
• Biological process: oxidation reduction (3 terms)
• Biochemical function: oxidoreductase activity (6 terms)

reference

DOI no: 10.1007/s00775-003-0485-0

J Biol Inorg Chem 8:843-854 (2003)

PubMed id: 14505072

X-ray structure of methanol dehydrogenase from Paracoccus denitrificans and molecular modeling of its interactions with cytochrome c-551i.

Z.X.Xia, W.W.Dai, Y.N.He, S.A.White, F.S.Mathews, V.L.Davidson.

ABSTRACT

The X-ray structure of methanol dehydrogenase (MEDH) from Paracoccus denitrificans (MEDH-PD) was determined at 2.5 A resolution using molecular replacement based on the structure of MEDH from Methylophilus methylotrophus W3A1 (MEDH-WA). The overall structures from the two bacteria are similar to each other except that the former has a longer C-terminal tail in each subunit and shows local differences in several insertion regions. The "X-ray sequence" of the segment alphaGly444-alphaLeu452 was established, including one insertion and seven replacements compared with the reported sequence. The primary electron acceptor of MEDH-PD is cytochrome c-551i (Cyt c551i). Based on the crystal structure of MEDH-PD and of the published structure of Cyt c551i, their interactions were investigated by molecular modeling. As a guide and starting point, the covalently attached cytochrome and PQQ domains of the alcohol dehydrogenase from Pseudomonas putida HK5 (ADH2B) were used. In the modeling, two molecules of Cyt c551i could be accommodated in their interaction with the MEDH heterotetramer in accordance with the two-fold molecular symmetry of the latter. Two models are proposed, in both of which electrostatic and hydrogen bonding interactions make major contributions to inter-protein binding. One of these models involves salt bridges from alphaArg99 of MEDH to the heme propionic acids of Cyt c551i and the other involves salt bridges from alphaArg426 of MEDH to Glu112 of Cyt c551i. Both involve salt bridges from alphaLys93 of MEDH to Asp75 of Cyt c551i. The size and nature of the cytochrome/quinoprotein heterodimer interfaces and calculations of electronic coupling and electron transfer rates favor one of these models over the other.