title: Mechanism of the reaction catalyzed by mandelate racemase: structure and mechanistic properties of the D270N mutant.
abstract: On the basis of the available high-resolution structures of mandelate racemase (MR) from Pseudomonas putida [Landro, J.A., Gerlt, J.A., Kozarich, J.W., Koo, C.W., Shah, V.J., Kenyon, G.L., Neidhart, D.J., Fujita, J., & Petsko, G.A. (1994) Biochemistry 33, 635-643], Lys 166 and His 297 are positioned appropriately to participate in catalysis as acid/base catalysts, with Lys 166 participating as the (S)-specific acid/base catalyst and His 297 participating as the (R)-specific acid/base catalyst. The dependence of kcat on pH for the racemization of both (R)- and (S)-mandelates suggests that the pKaS of the conjugate acids of Lys 166 and His 297 are both approximately 6.4 [Landro, J.A., Kallarakal, A.T., Ransom, S.C., Gerlt, J.A., Kozarich, J.W., Neidhart, D.J., Kenyon, G.L. (1991) Biochemistry 30, 9274-9281; Kallarakal, A.T., Mitra, B., Kozarich, J.W., Gerlt, J.A., Clifton, J.R., Petsko, G.A., & Kenyon, G.L. (1995) Biochemistry 34, 2788-2797]. Both acid/base catalysts are in close proximity to and approximately equidistant to the epsilon-ammonium group of Lys 164 and the essential Mg2+. The positive electrostatic potential provided by these cationic groups might be expected to increase the acidities of the cationic conjugate acids of the acid/base catalysts, thereby explaining the depressed pKa of Lys 166 but not the "normal" pKa of His 297. Asp 270 is hydrogen bonded of N delta of His 297 and, therefore, may allow the pKa of His 297 to be normal. In this paper we report the structural and mechanistic properties of the mutant in which Asp 270 is replaced with asparagine (D270N). The structure of D270N with (S)-atrolactate bound in the active site reveals no geometric alterations in the active site when compared to the structure of wild-type MR complexed with (S)-atrolactate, with the exception that the side chain of His 297 is tilted and displaced approximately 0.5 A away from Asn 270 and toward the (S)-atrolactate. The kcatS for both (R)- and (S)-mandelates are reduced approximately 10(4)-fold. In accord with the proposal that Asp 270 influences the pKa of His 297, in the (R)- to (S)-direction no ascending limb is detected in the dependence of kcat of pH; instead, kcat decreases from a low pH plateau as described by a pKa of 10. In the (S)- to (R)-direction the dependence of kcat of pH is a bell-shaped curve that is described by pKaS of 6.4 and 10. In analogy to the previously reported properties of the H297N mutant [Landro, J.A., Kallarakal, A.T., Ransom, S.C., Gerlt, J.A., Kozarich, J.W., Neidhart, D.J., & Kenyon, G.L. (1991) Biochemistry 30, 9274-9281], D270N catalyzes both the facile exchange of the alpha-proton of (S)- but not (R)-mandelate with solvent and the stereospecific elimination of bromide ion from (S)-p-(bromomethyl)mandalate. These observations suggest that His 297 and Asp 270 function as a catalytic dyad, with Asp 270 being at least partially responsible for the normal pKa of His 297 in wild-type MR.
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, USA.
authors.forename: S L
authors.initials: SL
authors.lastname: Schafer
authors.forename: W C
authors.initials: WC
authors.lastname: Barrett
authors.forename: A T
authors.initials: AT
authors.lastname: Kallarakal
authors.forename: B
authors.initials: B
authors.lastname: Mitra
authors.forename: J W
authors.initials: JW
authors.lastname: Kozarich
authors.forename: J A
authors.initials: JA
authors.lastname: Gerlt
authors.forename: J G
authors.initials: JG
authors.lastname: Clifton
authors.forename: G A
authors.initials: GA
authors.lastname: Petsko
authors.forename: G L
authors.initials: GL
authors.lastname: Kenyon
mesh_terms: D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002384:Catalysis; D004269:DNA, Bacterial / Q000235:genetics; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008333:Mandelic Acids / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D015394:Molecular Structure; D016297:Mutagenesis, Site-Directed; D017354:Point Mutation; D016958:Pseudomonas putida / Q000201:enzymology / Q000235:genetics; D019998:Racemases and Epimerases / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D012997:Solvents; D013237:Stereoisomerism
chemical_list: D004269:DNA, Bacterial; D008333:Mandelic Acids; D012997:Solvents; D019998:Racemases and Epimerases; C021540:mandelate racemase; C037938:mandelic acid