1ZCH

Structure of the hypothetical oxidoreductase YcnD from Bacillus subtilis

Summary for 1ZCH

• Entry DOI: 10.2210/pdb1zch/pdb
• Descriptor: Hypothetical oxidoreductase ycnD, CHLORIDE ION, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: nitroreductase, nadh-oxidase, oxidoreductase
• Biological source: Bacillus subtilis
• Total number of polymer chains: 1
• Total formula weight: 29260.23

Authors

Morokutti, A.,Lyskowski, A.,Sollner, S.,Pointner, E.,Fitzpatrick, T.B.,Kratky, C.,Gruber, K.,Macheroux, P. (deposition date: 2005-04-12, release date: 2005-11-01, Last modification date: 2023-10-25)

Primary citation

Morokutti, A.,Lyskowski, A.,Sollner, S.,Pointner, E.,Fitzpatrick, T.B.,Kratky, C.,Gruber, K.,Macheroux, P.
Structure and Function of YcnD from Bacillus subtilis, a Flavin-Containing Oxidoreductase(,).
Biochemistry, 44:13724-13733, 2005

PubMed Abstract: YcnD from the gram-positive bacterium Bacillus subtilis is a member of a family of bacterial proteins that act as NADH- and/or NADPH-dependent oxidoreductases. Here, we report for the first time on the biochemical characterization of the purified protein, demonstrating that YcnD is an FMN-containing enzyme that can be reduced by NADH or NADPH (Km = 6.4 and 4.4 microM, respectively). In the presence of free FMN as the electron-accepting substrate, the latter reductant showed a ping-pong Bi-Bi reaction mechanism, whereas utilization of NADH is competitively inhibited by this substrate. This finding suggests that NADPH is the physiological reductant of the enzyme. We also show that YcnD reduces nitro-organic compounds, chromate, and a series of azo dyes. The reduction of azo dyes appears to be mediated by free reduced FMN because the reaction is considerably slower in its absence. Structure determination by X-ray crystallography revealed that YcnD folds into a three layer alpha-beta-alpha sandwich strongly resembling the topology of the NADH oxidase superfamily. Similar to homologous bacterial oxidoreductase, YcnD forms homodimers with an extended dimer interface. The biochemical data and the structure are discussed in light of the putative physiological function of YcnD as an oxidoreductase delivering reduced FMN to enzymes that require the reduced cofactor for activity.

PubMed: 16229462
DOI: 10.1021/bi0510835

Experimental method

X-RAY DIFFRACTION (1.85 Å)