3U7R

FerB - flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from Paracoccus denitrificans

Summary for 3U7R

• Entry DOI: 10.2210/pdb3u7r/pdb
• Descriptor: NADPH-dependent FMN reductase, 1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL, NONAETHYLENE GLYCOL, ... (4 entities in total)
• Functional Keywords: alpha/beta twisted open-sheet, lavoprotein, quinone reductase, oxidoreductase
• Biological source: Paracoccus denitrificans
• Total number of polymer chains: 2
• Total formula weight: 44628.50

Authors

Marek, J.,Klumpler, T.,Sedlacek, V.,Kucera, I. (deposition date: 2011-10-14, release date: 2012-10-24, Last modification date: 2024-10-09)

Primary citation

Sedlacek, V.,Klumpler, T.,Marek, J.,Kucera, I.
The Structural and Functional Basis of Catalysis Mediated by NAD(P)H:acceptor Oxidoreductase (FerB) of Paracoccus denitrificans.
Plos One, 9:e96262-e96262, 2014

PubMed Abstract: FerB from Paracoccus denitrificans is a soluble cytoplasmic flavoprotein that accepts redox equivalents from NADH or NADPH and transfers them to various acceptors such as quinones, ferric complexes and chromate. The crystal structure and small-angle X-ray scattering measurements in solution reported here reveal a head-to-tail dimer with two flavin mononucleotide groups bound at the opposite sides of the subunit interface. The dimers tend to self-associate to a tetrameric form at higher protein concentrations. Amino acid residues important for the binding of FMN and NADH and for the catalytic activity are identified and verified by site-directed mutagenesis. In particular, we show that Glu77 anchors a conserved water molecule in close proximity to the O2 of FMN, with the probable role of facilitating flavin reduction. Hydride transfer is shown to occur from the 4-pro-S position of NADH to the solvent-accessible si side of the flavin ring. When using deuterated NADH, this process exhibits a kinetic isotope effect of about 6 just as does the NADH-dependent quinone reductase activity of FerB; the first, reductive half-reaction of flavin cofactor is thus rate-limiting. Replacing the bulky Arg95 in the vicinity of the active site with alanine substantially enhances the activity towards external flavins that obeys the standard bi-bi ping-pong reaction mechanism. The new evidence for a cryptic flavin reductase activity of FerB justifies the previous inclusion of this enzyme in the protein family of NADPH-dependent FMN reductases.

PubMed: 24817153
DOI: 10.1371/journal.pone.0096262

Experimental method

X-RAY DIFFRACTION (1.4 Å)