4hnc | pdb_00004hnc
P. putida C92S/K166C/C264S mandelate racemase co-crystallized with benzilic acid
Structural highlights
Publication Abstract from PubMedMandelate racemase (MR) from Pseudomonas putida catalyzes the Mg(2+)-dependent 1,1-proton transfer that interconverts the enantiomers of mandelate. Because trifluorolactate is also a substrate of MR, we anticipated that replacing the phenyl rings of the competitive, substrate-product analogue inhibitor benzilate (Ki = 0.7 mM) with trifluoromethyl groups might furnish an inhibitor. Surprisingly, the substrate-product analogue 3,3,3-trifluoro-2-hydroxy-2-(trifluoromethyl)propanoate (TFHTP) was a potent competitive inhibitor [Ki = 27 +/- 4 muM; cf. Km = 1.2 mM for both (R)-mandelate and (R)-trifluorolactate]. To understand the origins of this high binding affinity, we determined the X-ray crystal structure of the MR-TFHTP complex to 1.68 A resolution. Rather than chelating the active site Mg(2+) with its glycolate moiety, like other ground state analogues, TFHTP exhibited a novel binding mode with the two trifluoromethyl groups closely packed against the 20s loop and the carboxylate bridging the two active site Bronsted acid-base catalysts Lys 166 and His 297. Recognizing that positioning a carboxylate between the Bronsted acid-base catalysts could yield an inhibitor, we showed that tartronate was a competitive inhibitor of MR (Ki = 1.8 +/- 0.1 mM). The X-ray crystal structure of the MR-tartronate complex (1.80 A resolution) revealed that the glycolate moiety of tartronate chelated the Mg(2+) and that the carboxylate bridged Lys 166 and His 297. Models of tartronate in monomers A and B of the crystal structure mimicked the binding orientations of (S)-mandelate and that anticipated for (R)-mandelate, respectively. For the latter monomer, the 20s loop appeared to be disordered, as it also did in the X-ray structure of the MR triple mutant (C92S/C264S/K166C) complexed with benzilate, which was determined to 1.89 A resolution. These observations indicate that the 20s loop likely undergoes a significant conformational change upon binding (R)-mandelate. In general, our observations suggest that inhibitors of other enolase superfamily enzymes may be designed to capitalize on the recognition of the active site Bronsted acid-base catalysts as binding determinants. Potent inhibition of mandelate racemase by a fluorinated substrate-product analogue with a novel binding mode.,Nagar M, Lietzan AD, St Maurice M, Bearne SL Biochemistry. 2014 Feb 25;53(7):1169-78. doi: 10.1021/bi401703h. Epub 2014 Feb, 10. PMID:24472022[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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