PDBsum entry: 1yiq

Oxidoreductase

PDB id: 1yiq

Contents

Protein chain

684 a.a. *

Ligands

PQQ

HEM

PGR ×3

Metals

_CA

Waters ×485

* Residue conservation analysis

PDB id:

1yiq

Name:

Oxidoreductase

Title:

Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase adhiig from pseudomonas putida hk5. Compariison to the other quinohemoprotein alcohol dehydrogenase adhiib found in the same microorganism.

Structure:

Quinohemoprotein alcohol dehydrogenase. Chain: a. Ec: 1.1.99.-

Source:

Pseudomonas putida. Organism_taxid: 303. Strain: hk5

Resolution:

2.20Å R-factor: 0.173 R-free: 0.226

Authors:

H.Toyama,Z.W.Chen,M.Fukumoto,O.Adachi,K.Matsushita, F.S.Mathews

Key ref:

H.Toyama et al. (2005). Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADH-IIG from Pseudomonas putida HK5. J Mol Biol, 352, 91. PubMed id: 16061256 DOI: 10.1016/j.jmb.2005.06.078

Date:

12-Jan-05 Release date: 16-Aug-05

Protein chain

Q4W6G0  (Q4W6G0_PSEPU) -  Quinohemoprotein alcohol dehydrogenase ADH-IIG

Seq: 718 a.a.

Struc: 684 a.a.*

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

 Gene Ontology (GO) functional annotation 

• Cellular component: membrane (1 term)
• Biological process: oxidation reduction (1 term)
• Biochemical function: electron carrier activity (5 terms)

DOI no: 10.1016/j.jmb.2005.06.078

J Mol Biol 352:91 (2005)

PubMed id: 16061256

Molecular cloning and structural analysis of quinohemoprotein alcohol dehydrogenase ADH-IIG from Pseudomonas putida HK5.

H.Toyama, Z.W.Chen, M.Fukumoto, O.Adachi, K.Matsushita, F.S.Mathews.

ABSTRACT

Depending on the alcohols used as growth substrates, Pseudomonas putida HK5 produces two distinct quinohemoprotein alcohol dehydrogenases, ADH-IIB and ADH-IIG, both of which contain pyrroloquinoline quinone (PQQ) and heme c as the prosthetic groups but show different substrate specificities, especially for diol substrates. Molecular cloning of the gene of ADH-IIB and its crystal structure are already reported. Here, molecular cloning of the gene, qgdA, and solution of the three-dimensional structure of ADH-IIG are reported. The enzyme consists of 718 amino acid residues including a signal sequence of 29 amino acid residues. The PQQ domain is highly homologous to other quinoproteins, especially to quinohemoproteins. The crystal structure of ADH-IIG, determined at 2.2A resolution, shows that the overall structure and the amino acid residues involved in PQQ binding are quite similar to ADH-IIB and to another quinohemoprotein ADH, qhEDH from Comamonas testosteroni. However, the lengths of the linker regions connecting the PQQ and the cytochrome domains are different from each other, leading to a significant difference in orientation of the cytochrome domain with respect to the PQQ domain. Apart from ADH-IIB and qhEDH, ADH-IIG has an extra 12-residue helix within loop 3 in the PQQ domain and an extra 3(10) helix in the C terminus of the cytochrome domain, and both helices appear parallel and linked by a hydrogen bond. The amino acid residues contacting substrate/product in the crystal structures are also different among them. In the crystal structure of ADH-IIG with 1,2-propanediol, one of the hydroxyl groups of the substrate forms a hydrogen bond with O5 of PQQ and OD1 of Asp300, and the other interacts with a water molecule and with NE2 of Trp386, the corresponding residue of which is not found in ADH-IIB and qhEDH, and might be the residue responsible for making ADH-IIG prefer diol substrates.

Selected figure(s)

Figure 3.
Figure 3. Ribbon diagram of the ADH-IIG molecule. The PQQ and calcium ion are in the large b-propeller domain at the bottom and the heme group is in the small cytochrome domain at the top (the yellow helix on the top in the back belongs to the quinoprotein domain). The color ramps from blue at the N terminus to red at the C terminus. This diagram was prepared with MOLSCRIPT29 and rendered using Raster3-D.30

Figure 6.
Figure 6. Proposed hydride transfer mechanism for the oxidation of the substrate alcohol at the PQQ/Ca^2+ active site of ADH-IIG. Only a part of PQQ around the quinone moiety is shown. The grey sphere is the calcium ion. The proton of the hydroxyl group of the substrate is abstracted by either E178 or D300.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 352, 91-0) copyright 2005.

Figures were selected by an automated process.