3WHC

Crystal structure of a transcriptional regulator FadR from Bacillus subtilis in complex with stearoyl-CoA

Summary for 3WHC

• Entry DOI: 10.2210/pdb3whc/pdb
• Related: 1VI0 3WHB
• Descriptor: Fatty acid metabolism regulator protein, STEAROYL-COENZYME A (3 entities in total)
• Functional Keywords: transcriptional regulator, fatty acid degradation, transcription
• Biological source: Bacillus subtilis
• Cellular location: Cytoplasm : P94548
• Total number of polymer chains: 6
• Total formula weight: 138248.90

Authors

Fujihashi, M.,Nakatani, T.,Miki, K. (deposition date: 2013-08-23, release date: 2014-03-19, Last modification date: 2023-11-08)

Primary citation

Fujihashi, M.,Nakatani, T.,Hirooka, K.,Matsuoka, H.,Fujita, Y.,Miki, K.
Structural characterization of a ligand-bound form of Bacillus subtilis FadR involved in the regulation of fatty acid degradation.
Proteins, 82:1301-1310, 2014

PubMed Abstract: Bacillus subtilis FadR (FadR(Bs)), a member of the TetR family of bacterial transcriptional regulators, represses five fad operons including 15 genes, most of which are involved in β-oxidation of fatty acids. FadR(Bs) binds to the five FadR(Bs) boxes in the promoter regions and the binding is specifically inhibited by long-chain (C14-C20 ) acyl-CoAs, causing derepression of the fad operons. To elucidate the structural mechanism of this regulator, we have determined the crystal structures of FadR(Bs) proteins prepared with and without stearoyl(C18)-CoA. The crystal structure without adding any ligand molecules unexpectedly includes one small molecule, probably dodecyl(C12)-CoA derived from the Escherichia coli host, in its homodimeric structure. Also, we successfully obtained the structure of the ligand-bound form of the FadR(Bs) dimer by co-crystallization, in which two stearoyl-CoA molecules are accommodated, with the binding mode being essentially equivalent to that of dodecyl-CoA. Although the acyl-chain-binding cavity of FadR(Bs) is mainly hydrophobic, a hydrophilic patch encompasses the C1-C10 carbons of the acyl chain. This accounts for the previous report that the DNA binding of FadR(Bs) is specifically inhibited by the long-chain acyl-CoAs but not by the shorter ones. Structural comparison of the ligand-bound and unliganded subunits of FadR(Bs) revealed three regions around residues 21-31, 61-76, and 106-119 that were substantially changed in response to the ligand binding, and particularly with respect to the movements of Leu108 and Arg109. Site-directed mutagenesis of these residues revealed that Arg109, but not Leu108, is a key residue for maintenance of the DNA-binding affinity of FadR(Bs).

PubMed: 24356978
DOI: 10.1002/prot.24496

Experimental method

X-RAY DIFFRACTION (2.2 Å)