Characterization of a thermostable NADPH:FMN oxidoreductase from the mesophilic bacterium Bacillus subtilis.


The gene yhdA from Bacillus subtilis encoding a putative flavin mononucleotide (FMN)-dependent oxidoreductase was cloned and heterologously expressed in Escherichia coli. The purified enzyme has a noncovalently bound FMN cofactor, which is preferentially reduced by NADPH, indicating that YhdA is a NADPH:FMN oxidoreductase. The rate of NADPH oxidation is enhanced by the addition of external FMN, and analysis of initial rate measurements reveals the occurrence of a ternary complex in a bi-bi reaction mechanism. YhdA has also been shown to reductively cleave the -N=N- bond in azo dyes at the expense of NADPH, and hence, it possesses azoreductase activity, however, at a rate 100 times slower than that found for FMN. Using Cibacron Marine as a model compound, we could demonstrate that the dye is a competitive inhibitor of NADPH and FMN. The utilization of NADPH and the absence of a flavin semiquinone radical distinguish YhdA from flavodoxins, which adopt the same structural fold, i.e., a five-stranded beta sheet sandwiched by five alpha helices. The native molecular-mass of YhdA was determined to be 76 kDa, suggesting that the protein occurs as a tetramer, whereas the YhdA homologue in Saccharomyces cerevisiae (YLR011wp) forms a dimer in solution. Interestingly, the different oligomerization of these homologous proteins correlates to their thermostability, with YhdA exhibiting a melting point of 86.5 degrees C, which is 26.3 degrees C higher than that for the yeast protein. This unusually high melting point is proposed to be the result of increased hydrophobic packing between dimers and the additional presence of four salt bridges stabilizing the dimer-dimer interface. Study holds ProTherm entries: 20477, 20478 Extra Details: YhdA; azoreductase activity; hydrophobic packing; dimer-dimer interface

Submission Details

ID: gEgZWsfG

Submitter: Connie Wang

Submission Date: April 24, 2018, 8:52 p.m.

Version: 1

Publication Details
Deller S;Sollner S;Trenker-El-Toukhy R;Jelesarov I;G├╝bitz GM;Macheroux P,Biochemistry (2006) Characterization of a thermostable NADPH:FMN oxidoreductase from the mesophilic bacterium Bacillus subtilis. PMID:16752898
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)

Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1T0I 2004-04-09T00:00:00+0000 2.0 YLR011wp, a Saccharomyces cerevisiae NA(D)PH-dependent FMN reductase
5Y04 2017-07-14T00:00:00+0000 2.85 Crystal Structure of the complex between the vinculin D1 domain and alphaE-catenin
1SYQ 2004-04-01T00:00:00+0000 2.42 Human vinculin head domain VH1, residues 1-258, in complex with human talin's vinculin binding site 1, residues 607-636
2MWN 2014-11-13T00:00:00+0000 0 Talin-F3 / RIAM N-terminal Peptide complex
4DJ9 2012-02-01T00:00:00+0000 2.25 Human vinculin head domain Vh1 (residues 1-258) in complex with the talin vinculin binding site 50 (VBS50, residues 2078-2099)
6R9T 2019-04-04T00:00:00+0000 6.2 Cryo-EM structure of autoinhibited human talin-1
1NNI 2003-01-13T00:00:00+0000 2.5 Azobenzene Reductase from Bacillus subtilis
2GSW 2006-04-26T00:00:00+0000 2.92 Crystal Structure of the Putative NADPH-dependent Azobenzene FMN-Reductase YhdA from Bacillus subtilis, Northeast Structural Genomics Target SR135
3GFQ 2009-02-27T00:00:00+0000 3.0 Structure of YhdA, K109L variant
3GFR 2009-02-27T00:00:00+0000 2.4 Structure of YhdA, D137L variant

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 NAD(P)H-dependent FMN reductase LOT6 Q07923 LOT6_YEAST
100.0 FMN-dependent NADPH-azoreductase O07529 AZR_BACSU
100.0 B Vinculin P26039 TLN1_MOUSE
100.0 B Vinculin Q9Y490 TLN1_HUMAN
97.6 A Vinculin P85972 VINC_RAT
98.0 A Vinculin P26234 VINC_PIG
98.0 A Vinculin Q64727 VINC_MOUSE
98.0 A Vinculin P18206 VINC_HUMAN
100.0 A Vinculin P12003 VINC_CHICK