For present purposes, a protein-bound metal site consists of one or more metal ions and all protein side chain and exogenous bridging and terminal ligands that define the first coordination sphere of each metal ion. Such sites can be classified into five basic types with the indicated functions: (1) structural -- configuration (in part) of protein tertiary and/or quaternary structure; (2) storage -- uptake, binding, and release of metals in soluble form: (3) electron transfer -- uptake, release, and storage of electrons; (4) dioxygen binding -- metal-O{sub 2} coordination and decoordination; and (5) catalytic -- substrate binding, activation, and turnover. The authors present here a classification and structure/function analysis of native metal sites based on these functions, where 5 is an extensive class subdivided by the type of reaction catalyzed. Within this purview, coverage of the various site types is extensive, but not exhaustive. The purpose of this exposition is to present examples of all types of sites and to relate, insofar as is currently feasible, the structure and function of selected types. The authors largely confine their considerations to the sites themselves, with due recognition that these site features are coupled to protein structure at all levels. In themore » next section, the coordination chemistry of metalloprotein sites and the unique properties of a protein as a ligand are briefly summarized. Structure/function relationships are systematically explored and tabulations of structurally defined sites presented. Finally, future directions in bioinorganic research in the context of metal site chemistry are considered. 620 refs.« less

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Structural and Functional Aspects of Metal Sites in Biology

Mechanism of Molybdenum Nitrogenase.

Brian M. Hoffman,* Dmitriy Lukoyanov, Zhi-Yong Yang,† Dennis R. Dean,*,‡ and Lance C. Seefeldt*,† †Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, Utah 84322, United States ‡Department of Biochemistry, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States Departments of Chemistry and Molecular Biosciences, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States

Mechanism of Nitrogen Fixation by Nitrogenase: The Next Stage

This Account explores the catalytic reduction of dinitrogen by molybdenum complexes that contain the [HIPTN3N]3- ligand ([HIPTN3N]3- = [(HIPTNCH2CH2)3N]3-, where HIPT = 3,5-(2,4,6-i-Pr3C6H2)2C6H3) at room temperature and pressure with protons and electrons. A total of 7−8 equiv of ammonia is formed out of ∼12 possible (depending upon the Mo derivative employed). No hydrazine is formed. Numerous X-ray studies of proposed intermediates in the catalytic cycle suggest that N2 is being reduced at a sterically protected, single Mo center operating in oxidation states between MoIII and MoVI. Subtle variations of the [HIPTN3N]3- ligand are not as successful as a consequence of an unknown shunt in the catalytic cycle that consumes reduction equivalents to yield (it is proposed) dihydrogen.

https://science.sciencemag.org/content/sci/301/5629/76.full.pdf

Catalytic Reduction of Dinitrogen to Ammonia at a Single Molybdenum Center

Biological nitrogen fixation is mediated by the nitrogenase enzyme system that catalyses the ATP dependent reduction of atmospheric dinitrogen to ammonia. Nitrogenase consists of two component metalloproteins, the MoFe-protein with the FeMo-cofactor that provides the active site for substrate reduction, and the Fe-protein that couples ATP hydrolysis to electron transfer. An overview of the nitrogenase system is presented that emphasizes the structural organization of the proteins and associated metalloclusters that have the remarkable ability to catalyse nitrogen fixation under ambient conditions. Although the mechanism of ammonia formation by nitrogenase remains enigmatic, mechanistic inferences motivated by recent developments in the areas of nitrogenase biochemistry, spectroscopy, model chemistry and computational studies are discussed within this structural framework.

Structural Basis of Biological Nitrogen Fixation.

The crystal structure of the nitrogenase molybdenum-iron (MoFe) protein from Clostridium
pasteurianum (Cp1) has been determined at 3.0-A resolution by a combination of isomorphous replacement,
molecular replacement, and noncrystallographic symmetry averaging. The structure of Cp1, including the
two types of metal centers associated with the protein (the FeMo-cofactor and the P-cluster pair), is similar
to that previously described for the MoFe-protein from Azotobacter vinelandii (Av1). Unique features of
the Cpl structure arise from the presence of an ~50-residue insertion in the α subunit and an ~50-residue
deletion in the β subunit. As a consequence, the FeMo-cofactor is more buried in Cp1 than in Av1, since
the insertion is located on the surface above the FeMo-cofactor. The location of this insertion near the
putative nitrogenase iron protein binding site provides a structural basis for the observation that the nitrogenase
proteins from C. pasteurianum have low activity with complementary nitrogenase proteins isolated from
other organisms. Mechanistic implications of the Cp1 structure for substrate entry /product release,
substrate binding to the FeMo-cofactor, and electron- and proton-transfer reactions of nitrogenase are
discussed.

D. Woo

Papers

X-ray crystal structure of the nitrogenase molybdenum-iron protein from Clostridium pasteurianum at 3.0-A resolution.