Theoretical Insight to the Hydroxylamine Oxidoreductase Substrate Binding Site

FERNANDEZ, M.L.; DE BIASE, P.; BARI, S.E.; ESTRIN, D.

Roma, Italia

Conferencia; IInternational Conference on Porphyrins and Phtalocyanins 4; 2006

University of Rome “Tor Vergata”and Society of Porphyrins and Phthlocyanines.

Theoretical Insight to the Hydroxylamine Oxidoreductase Substrate Binding Site María Laura Fernández, Pablo de Biase, Sara E. Bari and Darío A. Estrin Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Inorgánica, Analítica y Química Física – INQUIMAE/CONICET, Ciudad Universitaria, Pabellón 2, C1428EHA  Nuñez, Buenos Aires, Argentina, dario@qi.fcen.uba.ar   The multiheme enzyme hydroxylamine oxidoreductase from the autotrophic bacteria Nitrosomonas europaea catalyzes the two steps conversion of hydroxilamine to nitrite, with the help of a complicate arrangement of heme groups. As a peculiar feature, this periplasmic protein has three subunits, linked with each other through a covalent bond between a C2 of a tyrosine residue of one subunit and a 5-meso carbon atom of c type heme of another, to form a homotrimer with a total of 24 heme groups. The linker meso substituted heme group is called P460, due to the absorbance of the ferrous form; the other seven hemes per subunit are c type hemes [1, 2]. The iron atom of the P460 heme is pentacoordinated in the ferric state, while the other c type hemes are in the low spin ferric state, hexacoordinated to two histidines each, forming an extraordinarily optimized electron transfer chain. The remarkable complexity of this scenario should be the starting point to explain the efficiency of both the catalytic reaction and energy storage [3]. In the present work, we focused on the influence of the peculiar monomeso pattern of substitution of the binding site (P460) in the efficient conversion of hydroxylamine to nitrite from a theoretical perspective, through electronic structure calculations at the density functional theory level (DFT), using the SIESTA code [4]. To start unraveling the participation on catalysis of the meso substituent, calculations on the stability of putative catalysis intermediates and on the nonplanar distortion modes of the P460 have been performed starting from the atomic resolution crystal structure of the protein [5]. Geometry optimizations of the P460 reaction intermediates proposed by Cabail et al [6] were used to calculate the dissociation energy of different nitrogen containing ligands (NH2OH, NO, HNO), considering the presence and absence of the meso tyrosine residue. The results indicate that the tyrosine residue enhances the binding of the natural substrate hydroxylamine, and benefits the stability of a FeIIINO intermediate, while it shows to behave indifferently in the FeIINO form. Characterization of the non planar heme distortions for the wildtype and for the protein without the covalent tyrosine-C2 bond were performed using the normal-coordinate structural decomposition procedure [7], and showed that the meso substituent induces a significant ruffling in all the intermediates considered, consistently with previous results in NO binding to heme models [8] and nitrophorins [9]. References 1. Hooper AB and Nason A. J. Biol. Chem. 1965; 240: 4044-57. 2. Arciero DM and Hooper AB. J. Biol. Chem. 1993; 268: 14645-54. 3. Kurnikov IV, Ratner MA and Pacheco VA. Biochemistry 2005; 44: 1856-63. 4. Soler JM, Artacho E, Gale J, García A, Junquera J, Ordejón P and Sánchez-Portal D. J. Phys: Condens. Matter 2002, 14: 2745. 5. Igarashi N, Moriyama H, Fuyiwara T, Fukuomori Y and Tanaka N. Nat. Struct. Biol. 1997, 4: 276-84. 6. Cabail MZ and Pacheco AA. Inorg. Chem. 2003; 42, 270-72. 7. Jentzen W, Song, X-Z and Shelnutt, JA. J. Phys. Chem. B 1997, 101: 1684. 8. Linker DP and Rodgers KR. Inorg. Chem. 2005, 44, 1367 9. Walker FA. J. Inorg. Biochem. 2005, 99, 216.