Database accession: MF7000526
Name: NfrA1 (Bacillus megaterium)
PDB ID: 5hdj
Experimental method: X-ray (1.89 Å)
Assembly: Homodimer
Source organism: Priestia megaterium
Primary publication of the structure:
Carles L, Besse-Hoggan P, Joly M, Vigouroux A, Moréra S, Batisson I
Functional and structural characterization of two Bacillus megaterium nitroreductases biotransforming the herbicide mesotrione.
(2016) Biochem. J. 473: 1443-53
PMID: 27005432
Abstract:
Mesotrione is a selective herbicide belonging to the triketone family, commonly used on maize cultures since 2003. A mesotrione-transforming Bacillus megaterium Mes11 strain isolated from an agricultural soil was used as a model to identify the key enzymes initiating the biotransformation of this herbicide. Two enzymes (called NfrA1 and NfrA2/YcnD) were identified, and functionally and structurally characterized. Both belong to the NfsA FRP family of the nitro-FMN reductase superfamily (type I oxygen-insensitive nitroreductase) and show optimal pH and temperature of 6-6.5 and 23-25°C, respectively. Both undergo a Ping Pong Bi Bi mechanism, with NADPH and NADPH/NADH as cofactors for NfrA1 and NfrA2/YcnD, respectively. It is interesting that both can also reduce various nitro compounds including pesticides, antibiotics, one prodrug and 4-methylsulfonyl-2-nitrobenzoic acid, one of the mesotrione metabolites retrieved from the environment. The present study constitutes the first identification of mesotrione-transforming enzymes. These enzymes (or their corresponding genes) could be used as biomarkers to predict the capacity of ecosystems to transform mesotrione and assess their contamination by both the parent molecule and/or the metabolites.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
nucleotide binding nucleotide binding
oxidoreductase activity oxidoreductase activity
Biological process: not assigned
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: NfrA1
Source organism: Priestia megaterium
Length: 249 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNSVIETILNHRSIRKYEDKPLSEEQIQTIVESAQAASTSSYIQAYSIIGVKDKETKRKLAQLAGNQPYVETNGHFFVFCADFHRHDVIAEMEKKDLSTALESTEQFMVAIIDVALAAQNATLAAESMGLGACYIGGLRNELEEVSKLLKLPHHVIPLFGLTVGHPAGITDKKPRLPFKHVYHEETYEPNDEQTKKELTAYNEEISAYYNERTNGKRQDTWTGQMAEMLSNPKRMYMKEFVEKQGFNKK
UniProtKB AC: A0A0K0VJM9 (positions: 2-248)
Coverage: 99%
Name: NfrA1
Source organism: Priestia megaterium
Length: 249 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMNSVIETILNHRSIRKYEDKPLSEEQIQTIVESAQAASTSSYIQAYSIIGVKDKETKRKLAQLAGNQPYVETNGHFFVFCADFHRHDVIAEMEKKDLSTALESTEQFMVAIIDVALAAQNATLAAESMGLGACYIGGLRNELEEVSKLLKLPHHVIPLFGLTVGHPAGITDKKPRLPFKHVYHEETYEPNDEQTKKELTAYNEEISAYYNERTNGKRQDTWTGQMAEMLSNPKRMYMKEFVEKQGFNKK
UniProtKB AC: A0A0K0VJM9 (positions: 1-248)
Coverage: 99%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Nitroreductase family
Evidence level: Indirect evidence
Evidence coverage: The full structure participates in mutual synergistic folding.
Complex Evidence:
Authors claim that the homodimeric NAD(P)H nitroreductase is a highly intertwined dimer with the FMN binding site lying at the dimer interface (PMID:18241886). Other structures belonging to the nitroreductase family also have an extensive interaction surface wherein a large hydrophobic solvent-accessible surface becomes buried upon dimer formation, suggesting that the monomers would be unstable on their own (PMID:16229462, PMID:19436071). Domain-swapping is also typical, where the extended C-terminal region extensively interacts with the core domain of the neighbouring monomer, forming an interlocked dimer (PMID:34473996, PMID:19436071, PMID:8885832).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
Download this entry's JSON file (.json)
