PDBsum entry 1ozk

Oxidoreductase

PDB id: 1ozk

Contents

Protein chain

385 a.a.

Ligands

FAD

NAD

Theoretical model

PDB id:

1ozk

Name:

Oxidoreductase

Title:

Theoretical model for nadh-ubiquinone reductase

Structure:

Nadh dehydrogenase. Chain: a. Synonym: nadh-ubiquinone dehydrogenase. Ec: 1.6.99.3

Source:

Escherichia coli. Bacteria

Authors:

R.Schmid,D.L.Gerloff

Key ref:

R.Schmid and D.L.Gerloff (2004). Functional properties of the alternative NADH:ubiquinone oxidoreductase from E. coli through comparative 3-D modelling. FEBS Lett, 578, 163-168. PubMed id: 15581635 DOI: 10.1016/j.febslet.2004.10.093

Date:

09-Apr-03 Release date: 24-Aug-04

Protein chain

P00393  (DHNA_ECOLI) -  NADH dehydrogenase from Escherichia coli (strain K12)

Seq: 434 a.a.

Struc: 385 a.a.

DOI no: 10.1016/j.febslet.2004.10.093

FEBS Lett 578:163-168 (2004)

PubMed id: 15581635

Functional properties of the alternative NADH:ubiquinone oxidoreductase from E. coli through comparative 3-D modelling.

R.Schmid, D.L.Gerloff.

ABSTRACT

The alternative NADH:ubiquinone oxidoreductase (NDH-2) from Escherichia coli is a membrane protein playing a prominent role in respiration by linking the reduction of NADH to the quinone pool. Remote sequence similarity reveals an evolutionary relation between alternative NADH:quinone oxidoreductases and the SCOP-family "FAD/NAD-linked reductases". We have created a structural model for NDH-2 from E. coli through comparative modelling onto a template from this family. Combined analysis of our model and sequence conservation allowed us to include the cofactor FAD and the substrate NADH in atomic detail. Furthermore, we propose the most plausible orientation of NDH-2 relative to the membrane and specify a region of the protein potentially involved in ubiquinone binding.

Selected figure(s)

Figure 2.
Fig. 2. Detailed views of the FAD binding site (A) and the NADH binding site (B). Displayed are all protein residues within 3.3 Å of FAD or NADH that are likely to be involved in hydrogen bonding to these cofactors. Atoms are coloured according to CPK (carbon-white; oxygen-red; nitrogen-blue; phosphorous-orange), carbon atoms in FAD and NADH are depicted in green for better distinction. The side chain of Arg40 was omitted for clarity. Predicted hydrogen bonds between protein and FAD or NADH are indicated by dotted lines. The figure was produced using SYBYL 6.8 (Tripos Associates, St. Louis).

Figure 3.
Fig. 3. Helix-wheel representations of the two predicted C-terminal helices (Panel A: Arg390–Ala406; Panel B: Gly409–Arg424) for the NDH-2 subfamily alignment (E-value cutoff 10^−30, with respect to E. coli NDH-2). Two distinguishable groups are treated separately; sequences belonging to the DHNA_ECOLI group are displayed on the outside of the helix wheel, sequences belonging to the YLID_BACSU group on the inside. The groups consist of 14 and 13 sequences, respectively. Different font sizes denote the number of occurrences of the respective residue in the alignment (1–2; 3–5; 6–10; >10). The colouring scheme matches physical properties of the residues at each position; blue boxes correspond to predominantly positively charged residues; light blue boxes to predominantly hydrophilic residues, yellow boxes to predominantly hydrophobic residues and violet boxes to Trp, Tyr and His, i.e. polar aromatic residues which are potentially important for membrane binding.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS Lett (2004, 578, 163-168) copyright 2004.

Figures were selected by an automated process.