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Structural and Functional Aspects of Metal Sites in Biology

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Structural and Functional Aspects of Metal Sites in Biology + + Chem. Rev. 1996, 96, 2239−2314 2239 Structural and Functional Aspects of Metal Sites in Biology Richard H. Holm,*,† Pierre Kennepohl,‡ and Edward I. Solomon*,‡ Departments of Chemistry, Harvard University, Cambridge, Massachusetts 02138, and Stanford University, Stanford, California 94305 Received June 10, 1996 (Revised Manuscript Received September 3, 1996) Contents (ii) storagesuptake, binding, and release of metals in soluble form; I. Introduction 2239 (iii) electron transfersuptake, release, and storage II. Metallobiomolecules as Elaborated Inorganic 2239 of electrons; Complexes (iv) dioxygen bindingsmetal-O2 coordination and A. Coordinated Ligands 2240 decoordination; B. Unique Properties of a Protein Ligand 2246 (v) catalyticssubstrate binding, activation, and C. Physical Methods 2250 turnover. III. Active-Site Structure/Function Relationships 2251 We present here a classification and structure/ A. Electron Transfer 2251 function analysis of native metal sites based on these B. Dioxygen Binding 2263 functions, where v is an extensive class subdivided C. Superoxide and Peroxide Dismutases and 2270 by the type of reaction catalyzed (dismutases, oxi- Non-Heme Peroxidases dases and oxygenase, nitrogenases and hydrogen- D. Oxidases and Oxygenases 2275 ases, oxotransferases, hydrolases, and others). In E. Hydrogenases and Nitrogenases 2287 order to restrict the scope of information presented F. Oxotransferases 2293 to a manageable size, sites containing heme and G. Transport and Storage Proteins 2296 corrin units have been excluded with only several H. Nonredox Enzymes 2300 exceptions. Here, structure refers primarily to crys- tallographic information. Not included in the tabula- IV. Prospectus 2306 tions of site structures which follow are (partial) V. References 2307 structural deductions from X-ray absorption spec- troscopy, NMR, and other spectroscopic techniques. Within this purview, coverage of the various site I. Introduction types is extensive, but not exhaustive. The purpose The field of bioinorganic chemistry is at a propi- of this exposition is to present examples of all types tious stage of development. Ever more complex of sites and to relate, insofar as is currently feasible, metallobiomolecules are isolated and purified, physi- the structure and function of selected types. Func- cal methodologies and attendant theories probe even tional aspects of the latter and other sites are the more deeply into the intricacies of electronic structure subjects of accompanying contributions in this issue. and structural dynamics, chemical syntheses of pro- We largely confine our considerations to the sites tein and metal coordination units become more themselves, with due recognition that these site sophisticated, and biochemical syntheses with site- features are coupled to protein structure at all levels. directed mutagenesis disclose functions of specific In the next section, the coordination chemistry of amino acid residues. Inasmuch as explication of metalloprotein sites and the unique properties of a function is the ultimate investigative goal of any protein as a ligand are briefly summarized. In biological process, and function is inseparable from section III, structure/function relationships are sys- geometric structure, the ever-increasing crystallo- tematically explored and tabulations of structurally graphic database of protein structure assumes an defined sites presented. Other compilations of met- even greater significance. One need only contem- alloprotein structures have been made earlier.6 Fi- plate the active-site structures of, inter alia, such nally, in section IV, future directions in bioinorganic complex molecules as nitrogenase,1 cytochrome c research in the context of metal site chemistry are oxidase,2,3 sulfite reductase,4 and ceruloplasmin5 considered. Throughout, it will be evident that a reported within the last four years, to recognize that high-resolution metalloprotein structure provides the these can now be conceived at a molecular level of initial point for penetrating the complexities of site detail. For present purposes, a protein-bound metal function. But as such, it is only the beginning, and site consists of one or more metal ions and all protein not the end, of any inquiry into function. side chain and exogenous bridging and terminal ligands that define the first coordination sphere of II. Metallobiomolecules as Elaborated Inorganic each metal ion. Such sites can be classified into five Complexes basic types with the indicated functions: (i) structuralsconfiguration (in part) of protein Of the 4048 protein crystal structures contained tertiary and/or quaternary structure; in the Brookhaven Protein Data Bank as of December 1995, 2123 (52%) contain metals (excluding weakly 7 † Harvard University. bound metals such as sodium). This count includes ‡ Stanford University. proteins and enzymes with heme and corrin groups S0009-2665(95)00039-2 CCC: $25 00 © 1996 American Chemical Society + + 2240 Chemical Reviews, 1996, Vol. 96, No. 7 Holm et al. Richard H. Holm was born in Boston, MA, spent his younger years on Edward I. Solomon grew up in North Miami Beach, FL, received his Ph.D. Nantucket Island and Cape Cod, and graduated from the University of from Princeton University (with D. S. McClure), and was a postdoctoral Massachusetts (B.S.) and Massachusetts Institute of Technology (Ph.D.). fellow at the H. C. Ørsted Institute (with C. J. Ballhausen) and then at He has served on the faculties of the University of Wisconsin, the Caltech (with H. B. Gray). He was a professor at the Massachusetts Massachusetts Institute of Technology, and Stanford University. Since Institute of Technology until 1982, when he moved to Stanford University, 1980 he has been at Harvard University, where he has been Chairman where he is now the Monroe E. Spaght Professor of Humanities and of the Department of Chemistry, and since 1983 Higgins Professor of Sciences. His research is in the fields of physical−inorganic and Chemistry. His research interests are centered in inorganic and bioinorganic chemistry with emphasis on the application of a wide variety bioinorganic chemistry, with particular reference to the synthesis of of spectroscopic methods to elucidate the electronic structure of transition molecules whose structures and reactions are pertinent to biological metal complexes and its contribution to physical properties and reactivity. processes. Metals which occur in the five types of sites above, or can be substituted for the native constituent, are “biological” metals. This set includes magnesium, calcium, all members of the first transition series (excluding scandium, titanium, and chromium), and molybdenum, tungsten, cadmium, and mercury. These metals and their ligands constitute prosthetic groups that usually are covalently bound to the polypeptide backbone by endogenous ligands pro- vided by amino acid side chains. As initial examples, consider the structures of the electron-transfer pro- teins plastocyanin and rubredoxin in Figure 1. Shown are the single-chain protein structures and, in mag- nified form, the [CuII(N‚His)(S‚Met)(S‚Cys)] and [FeIII- (S‚Cys)4] active sites. These depictions illustrate the protein structures which, although somewhat com- Pierre Kennepohl was born Dec 12, 1970, in Scarborough, Canada, plicated, reduce in each case to a spatially correlated although he has spent most of his life in Montre´al, Canada, which he tetradentate ligand. Protein structure and environ- considers home. Pierre completed his B.Sc. in chemistry at Concordia University in Montre´al as a member of its Institute for Cooperative ment modulate properties such as electronic struc- Education, which provided him with research opportunities in several areas ture, redox potential, and detailed stereochemistry, including enzymology, solid-state chemistry, and pulse radiolysis. He was some or all of which in the general case will depart also fortunate to study under Professor Nick Serpone at Concordia, where from the intrinsic value of the coordination unit he studied the photochemical and photophysical properties of surface- removed from the protein and allowed to relax to its modified TiO2. Pierre is currently working toward his Ph.D. in inorganic energy minimum. It is in this sense that a metallo- chemistry at Stanford under the guidance of Professor Edward I. Solomon, with financial support from NSERC (Canada) in the form of a 1967 Science biomolecule is an elaborated metal complex. In this & Engineering Scholarship. His research interests include the elucidation section, we focus on metal ion active sites and of detailed electronic structure contributions to electron transfer processes consider the properties of the protein as a unique in iron−sulfur centers and other redox-active metal sites in biology. He ligand. also enjoys any opportunity to involve himself in the teaching of chemistry and is presently a teaching consultant at Stanford. When not worrying A. Coordinated Ligands about things like electronic relaxation and redox potentials, Pierre likes to spend time playing and writing music and getting involved in It is important first to recognize metallobiomol- departmental affairs. ecules in which a metal is enclosed by a macrocylic ligand that forms the equatorial plane of coordina- and is biased by the inclusion of mutated forms of tion. These include heme and corrin units, which certain metallobiomolecules and structures of the may be either covalently or noncovalently (through same enzyme with different
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