Database accession: MF7000532
Name: FMN and NADPH-dependent nitroreductase NfnB (Sphingopyxis sp. strain HMH)
PDB ID: 7dp0
Experimental method: X-ray (2.10 Å)
Assembly: Homodimer
Source organism: Sphingopyxis sp MG
Primary publication of the structure:
Kim SH, Park S, Park E, Kim JH, Ghatge S, Hur HG, Rhee S
Structure and substrate specificity determinants of NfnB, a dinitroaniline herbicide-catabolizing nitroreductase from Sphingopyxis sp. strain HMH.
(2021) J. Biol. Chem. 297: 101143
PMID: 34473996
Abstract:
Nitroreductases are emerging as attractive bioremediation enzymes, with substrate promiscuity toward both natural and synthetic compounds. Recently, the nitroreductase NfnB from Sphingopyxis sp. strain HMH exhibited metabolic activity for dinitroaniline herbicides including butralin and pendimethalin, triggering the initial steps of their degradation and detoxification. However, the determinants of the specificity of NfnB for these herbicides are unknown. In this study, we performed structural and biochemical analyses of NfnB to decipher its substrate specificity. The homodimer NfnB is a member of the PnbA subgroup of the nitroreductase family. Each monomer displays a central α + β fold for the core domain, with a protruding middle region and an extended C-terminal region. The protruding middle region of Val75-Tyr129 represents a structural extension that is a common feature to members of the PnbA subgroup and functions as an opening wall connecting the coenzyme FMN-binding site to the surface, therefore serving as a substrate binding site. We performed mutational, kinetic, and structural analyses of mutant enzymes and found that Tyr88 in the middle region plays a pivotal role in substrate specificity by determining the dimensions of the wall opening. The mutation of Tyr88 to phenylalanine or alanine caused significant changes in substrate selectivity toward bulkier dinitroaniline herbicides such as oryzalin and isopropalin without compromising its activity. These results provide a framework to modify the substrate specificity of nitroreductase in the PnbA subgroup, which has been a challenging issue for its biotechnological and bioremediation applications.
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: Nitroreductase family protein
Source organism: Sphingopyxis sp MG
Length: 233 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMPATDTLSLSASEALARRRSVRAFTDRPVDRALLARIFEIAQRAPSGGNLQPWQATVVTGERWQAVQDAVAARIVMGREGFQPEYDIYPRGLTDPWDSRRFGVGEALYASLGIARDDKAGRIAQFQQNYRGFGAPVMLFLHCSRIMGPPQWADMGMWLQSVMLLLVEHGLASCPQECWAMYGATVRAELGLGDDQILFSGLAIGHADEEAPVNRWPVPRVGLDEVIDWQGFDA
UniProtKB AC: A0A2L0VUJ4 (positions: 9-231)
Coverage: 95%
Name: Nitroreductase family protein
Source organism: Sphingopyxis sp MG
Length: 233 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMPATDTLSLSASEALARRRSVRAFTDRPVDRALLARIFEIAQRAPSGGNLQPWQATVVTGERWQAVQDAVAARIVMGREGFQPEYDIYPRGLTDPWDSRRFGVGEALYASLGIARDDKAGRIAQFQQNYRGFGAPVMLFLHCSRIMGPPQWADMGMWLQSVMLLLVEHGLASCPQECWAMYGATVRAELGLGDDQILFSGLAIGHADEEAPVNRWPVPRVGLDEVIDWQGFDA
UniProtKB AC: A0A2L0VUJ4 (positions: 9-231)
Coverage: 95%
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)
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