PDBsum entry 1z48

Oxidoreductase

PDB id: 1z48

Contents

Protein chains

337 a.a. *

Ligands

FMN ×2

Waters ×669

* Residue conservation analysis

PDB id:

1z48

Name:

Oxidoreductase

Title:

Crystal structure of reduced yqjm from bacillus subtilis

Structure:

Probable nadh-dependent flavin oxidoreductase yqjm. Chain: a, b. Synonym: yqjm. Engineered: yes

Source:

Bacillus subtilis. Organism_taxid: 1423. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Tetramer (from PDB file)

Resolution:

1.80Å R-factor: 0.179 R-free: 0.199

Authors:

K.Kitzing,T.B.Fitzpatrick,C.Wilken,J.Sawa,G.P.Bourenkov,P.Macheroux, T.Clausen

Key ref:

K.Kitzing et al. (2005). The 1.3 A crystal structure of the flavoprotein YqjM reveals a novel class of Old Yellow Enzymes. J Biol Chem, 280, 27904-27913. PubMed id: 15890652 DOI: 10.1074/jbc.M502587200

Date:

15-Mar-05 Release date: 17-May-05

Protein chains

P54550  (NAMA_BACSU) -  NADPH dehydrogenase from Bacillus subtilis (strain 168)

Seq: 338 a.a.

Struc: 337 a.a.

Enzyme reactions

• Enzyme class: E.C.1.6.99.1 - Nadph dehydrogenase.
• Reaction: A + NADPH + H⁺ = AH2 + NADP⁺
• Cofactor: FMN or FAD

FMN (Bound ligand (Het Group name = FMN) corresponds exactly) or FAD

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

reference

DOI no: 10.1074/jbc.M502587200

J Biol Chem 280:27904-27913 (2005)

PubMed id: 15890652

The 1.3 A crystal structure of the flavoprotein YqjM reveals a novel class of Old Yellow Enzymes.

K.Kitzing, T.B.Fitzpatrick, C.Wilken, J.Sawa, G.P.Bourenkov, P.Macheroux, T.Clausen.

ABSTRACT

Here we report the crystal structure of YqjM, a homolog of Old Yellow Enzyme (OYE) that is involved in the oxidative stress response of Bacillus subtilis. In addition to the oxidized and reduced enzyme form, the structures of complexes with p-hydroxybenzaldehyde and p-nitrophenol, respectively, were solved. As for other OYE family members, YqjM folds into a (alpha/beta)8-barrel and has one molecule of flavin mononucleotide bound non-covalently at the COOH termini of the beta-sheet. Most of the interactions that control the electronic properties of the flavin mononucleotide cofactor are conserved within the OYE family. However, in contrast to all members of the OYE family characterized to date, YqjM exhibits several unique structural features. For example, the enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers. Moreover, the protein displays a shared active site architecture where an arginine finger (Arg336) at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal Tyr28 instead of a COOH-terminal tyrosine in OYE and its homologs. The structural information led to a specific data base search from which a new class of OYE oxidoreductases was identified that exhibits a strict conservation of active site residues, which are critical for this subfamily, most notably Cys26, Tyr28, Lys109, and Arg336. Therefore, YqjM is the first representative of a new bacterial subfamily of OYE homologs.

Selected figure(s)

Figure 3.
FIG. 3. The flavin binding site. A, stereo view of the flavin binding site. The final 1.3 Å resolution 2F[o] - F[c] map is contoured at 1.5 . The flavin and the side chains of the amino acids are drawn in ball-and-stick mode, with FMN in yellow and the residues from monomer A in gray and from the neighboring monomer B in violet. B, schematic illustration of the interaction of FMN with active site residues. The thin red dotted lines illustrate hydrogen bonds.

Figure 4.
FIG. 4. Electron density map of Cys26 and Tyr28 in the active site. The 3F[o] - 2F[c] map is contoured at 1.2 . Amino acids and FMN are presented as in Fig. 3.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 27904-27913) copyright 2005.

Figures were selected by an automated process.