PDBsum entry 1kb0

Oxidoreductase

PDB id: 1kb0

Contents

Protein chain

670 a.a. *

Ligands

HEC

TFB

PQQ

GOL ×3

Metals

_CA

Waters ×1020

* Residue conservation analysis

PDB id:

1kb0

Name:

Oxidoreductase

Title:

Crystal structure of quinohemoprotein alcohol dehydrogenase from comamonas testosteroni

Structure:

Quinohemoprotein alcohol dehydrogenase. Chain: a. Synonym: quinohemoprotein ethanol dehydrogenase type 1. Ec: 1.1.99.-

Source:

Comamonas testosteroni. Organism_taxid: 285

Resolution:

1.44Å R-factor: 0.160 R-free: 0.188

Authors:

H.J.Rozeboom,A.Oubrie

Key ref:

A.Oubrie et al. (2002). Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni: structural basis for substrate oxidation and electron transfer. J Biol Chem, 277, 3727-3732. PubMed id: 11714714 DOI: 10.1074/jbc.M109403200

Date:

05-Nov-01 Release date: 28-Dec-01

Protein chain

Q46444  (QHED_COMTE) -  Quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni

Seq: 708 a.a.

Struc: 670 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.1.9.1 - alcohol dehydrogenase (azurin).
• Reaction: 2 oxidized [azurin] + a primary alcohol = 2 reduced [azurin] + an aldehyde + 2 H⁺
• Cofactor: Heme; Pyrroloquinoline quinone

Heme (Bound ligand (Het Group name = HEC) matches with 95.45% similarity) Pyrroloquinoline quinone (Bound ligand (Het Group name = PQQ) corresponds exactly)

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

reference

DOI no: 10.1074/jbc.M109403200

J Biol Chem 277:3727-3732 (2002)

PubMed id: 11714714

Crystal structure of quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni: structural basis for substrate oxidation and electron transfer.

A.Oubrie, H.J.Rozeboom, K.H.Kalk, E.G.Huizinga, B.W.Dijkstra.

ABSTRACT

Quinoprotein alcohol dehydrogenases are redox enzymes that participate in distinctive catabolic pathways that enable bacteria to grow on various alcohols as the sole source of carbon and energy. The x-ray structure of the quinohemoprotein alcohol dehydrogenase from Comamonas testosteroni has been determined at 1.44 A resolution. It comprises two domains. The N-terminal domain has a beta-propeller fold and binds one pyrroloquinoline quinone cofactor and one calcium ion in the active site. A tetrahydrofuran-2-carboxylic acid molecule is present in the substrate-binding cleft. The position of this oxidation product provides valuable information on the amino acid residues involved in the reaction mechanism and their function. The C-terminal domain is an alpha-helical type I cytochrome c with His(608) and Met(647) as heme-iron ligands. This is the first reported structure of an electron transfer system between a quinoprotein alcohol dehydrogenase and cytochrome c. The shortest distance between pyrroloquinoline quinone and heme c is 12.9 A, one of the longest physiological edge-to-edge distances yet determined between two redox centers. A highly unusual disulfide bond between two adjacent cysteines bridges the redox centers. It appears essential for electron transfer. A water channel delineates a possible pathway for proton transfer from the active site to the solvent.

Selected figure(s)

Figure 4.
Fig. 4. Proposed reaction mechanisms for substrate conversion by QH-ADH. A, alcohol oxidation. The reactive C5 atom of PQQ is indicated by the number 5. B, aldehyde oxidation.

Figure 5.
Fig. 5. Proposed pathways for electron and proton transfer. A, electron transfer. Optimal pathways and one longer alternative are indicated. B, proton transfer. Hydrogen bonds are visualized by black dotted lines. The gap in the hydrogen-bonding pattern is indicated. Residues possibly involved in either pathway are shown as ball-and-stick models.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 3727-3732) copyright 2002.

Figures were selected by the author.