Structural basis of substrate recognition by the substrate binding protein (SBP) of a hydrazide transporter, obtained from Microbacterium hydrocarbonoxydans

• Published in: Biochemical and biophysical research communications Vol. 525; no. 3; pp. 720 - 725
• Main Authors: Shimamura, Kaho, Akiyama, Tomonori, Yokoyama, Kazuhiro, Takenoya, Mihoko, Ito, Shinsaku, Sasaki, Yasuyuki, Yajima, Shunsuke
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 07.05.2020
• Subjects: ABC transporter; Conformation change; Ligand specificity; X-ray crystal structure; Conformation change; Ligand specificity; X-ray crystal structure; ABC transporter
• ISSN: 0006-291X; 1090-2104
• DOI: 10.1016/j.bbrc.2020.02.146

Microbacterium hydrocarbonoxydans was isolated, using hydrazide compounds as its sole carbon source. The key enzyme that metabolizes these compounds was identified as hydrazidase, and the operon containing the gene coding for the enzyme, was revealed by genome sequencing. The operon also contained genes coding for an ATP-binding cassette transporter (ABC transporter), which was expected to transport the hydrazide compounds. Substrate binding protein (SBP), a component subunit of the transporter, plays an important role in recognizing the correct substrates for transport. Therefore, to elucidate the mechanism of recognition of the unnatural hydrazide compounds, we determined the crystal structures of the SBP, obtained from M. hydrocarbonoxydans (Mh-SBP), complexed with and without the hydrazide compound, at 2.2 Å and 1.75 Å resolutions, respectively. The overall structures of Mh-SBP were similar to those of the SBP in oligopeptide transporters such as OppA. On comparison, the liganded and unliganded structures of Mh-SBP showed an open – close conformation change. Interestingly, the binding mode of the compound to Mh-SBP was almost identical to that of the compound to hydrazidase, suggesting that the ABC transporter served transporting these compounds. Furthermore, based on the hydrazide complex structure, paraben, the other putative substrate of the protein, was successfully used with Mh-SBP to obtain the paraben complex structure. [Display omitted] •Crystal structures of the SBP of an ABC transporter were determined.•The oligopeptide-annotated binding protein bound to an unnatural hydrazide compound.•The liganded structures suggested the specificity determinant structure for ligands.•Based on the hydrazide-complex, a paraben complex structure was developed.•Results suggested that the SBP showed novel substrate specificity in Cluster C.