7dp2 | pdb_00007dp2

Crystal structure of FMN and NADPH-dependent nitroreductase NfnB mutant Y88F derived from sphigopyxis sp. strain HMH

spinqualitylabelsall models 7dp2, resolution 2.40Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7dp2 is a 2 chain structure with sequence from Sphingopyxis sp.. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.4000874Å Ligands: FMN Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function A0A2L0VUJ4_9SPHN Publication Abstract from PubMed 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 alpha + beta 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. Structure and substrate specificity determinants of NfnB, a dinitroaniline herbicide-catabolizing nitroreductase from Sphingopyxis sp. strain HMH.,Kim SH, Park S, Park E, Kim JH, Ghatge S, Hur HG, Rhee S J Biol Chem. 2021 Oct;297(4):101143. doi: 10.1016/j.jbc.2021.101143. Epub 2021, Aug 30. PMID:34473996 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Nitroreductase 3D structures

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