These studies demonstrate that the chemical nature of the direct ligands and the structure of the surrounding hydrogen bond network are crucial for both the activity of carbonic anhydrase and the metal ion affinity of the zinc-binding site. An understanding of naturally occurring zinc-binding sites will aid in creating de novo zinc-binding proteins and in designing new metal sites in existing proteins for novel purposes such as to serve as metal ion biosensors.
Zinc was first shown to be required for the growth of the mold Aspergillus niger by Raulin in Since then, zinc has been demonstrated to be essential for the growth, development and differentiation of all types of life, including microorganisms, plants and animals Vallee After iron, zinc is the second most abundant trace metal in the human body; an average kg adult human contains 2. In most cases, the zinc ion is an essential cofactor for the observed biological function of these metalloenzymes.
Furthermore, the biological functions of zinc, which are versatile and observed in many tissues, are most often associated with proteins. The inherent chemical potential and reactivity of zinc are not exceptional compared with those of other metals Cotton and Wilkinson However, unlike other first-row transition metals e. Therefore, the zinc ion is an ideal metal cofactor for reactions that require a redox-stable ion to function as a Lewis acid—type catalyst Butler , such as proteolysis and the hydration of carbon dioxide. Nevertheless, in all zinc metalloenzymes studied to date, the binding geometry observed most often is a slightly distorted tetrahedral Scheme 1 with the metal ion coordinating three or four protein side chains.
However, five-coordinate distorted trigonal bipyramidal geometry has been observed in the metal sites of Zn-substituted astacin EC 3. In addition, five-coordinate geometry has been suggested for the reaction intermediate in CA Christianson and Fierke , Lindskog and carboxypeptidase A EC 3. Early examinations of the coordination preferences of zinc ions concluded that zinc preferentially bound to sulfur ligands due to the predominance of zinc sulfides in zinc ores, e.
In protein zinc-binding sites, the zinc ion is coordinated by different combinations of protein side chains, including the nitrogen of histidine, the oxygen of aspartate or glutamate and the sulfur of cysteine; among these, histidine is most commonly observed, followed by cysteine Gregory et al. Other, much more rarely observed ligands include the hydroxyl of tyrosine, the carbonyl oxygen of the protein backbone and the carbonyl oxygen of either asparagine or glutamine.
The varied ligands and coordination geometries in zinc metalloenzymes result in zinc-binding sites with a broad range of stability constants, reactivities and functions.
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Comparison of the zinc ligands L 1 , L 2 , L 3 and L 4 and the spacers X, Y and Z between zinc ligands in catalytic and structural zinc sites 1. Included in this table are representative enzymes in which the active site ligands differ. The protein ligands are shown using the one-letter amino acid codes of: H, histidine; C, cysteine; D, aspartate; and E, glutamate. The relatively long spacer between L 1 and L 2 is unusual, and it may be due to the requirements of NAD H cofactor binding at the active site.
Not available. The zinc ligands were determined by mutations that abolish both the zinc-binding affinity and the catalytic activity. The zinc site of carbonic anhydrase of M. References: 3 Cedergren-Zeppezauer et al. In zinc proteins, the major role of the zinc ion can be catalytic, cocatalytic or structural. In a catalytic zinc site, the zinc ion directly participates in the bond-making or -breaking step. In a cocatalytic zinc site, there are several metal ions bound in proximity to one another, where one plays a catalytic role and the other metal ions enhance the catalytic activity of the site Vallee and Auld a.
Finally, in structural zinc sites, the zinc ion mainly stabilizes the tertiary structure of the enzyme in a manner analogous to disulfide bonds. In all cases, removal of the bound zinc can lead to a loss of enzymatic activity. A systematic analysis of the structure and function of a number of zinc proteins has established distinct features of catalytic and structural zinc sites, as described later Table 2 Arnold and Haymore , Coleman , Vallee and Auld a , b. As understanding of the biochemical role of zinc in these biological macromolecules increases, the connection between the detailed biochemical functions and physiological phenotypes can be established.
Vallee and Auld b. Vallee and Auld a.
A catalytic zinc ion is located at the active site of an enzyme, where it participates directly in the catalytic mechanism, interacting with the substrate molecules undergoing reaction. A unique feature for a catalytic zinc site is the existence of an open coordination sphere; that is, the zinc-binding polyhedron contains at least one water molecule in addition to three or four protein ligands Vallee and Auld a , b.
This feature is diagnostic of a catalytic zinc site compared with a structural zinc site, where the metal polyhedron is saturated with protein side chains and this difference can be detected by a number of spectroscopic and structural techniques. The zinc-bound water is a critical component for a catalytic zinc site, because it can be either ionized to zinc-bound hydroxide as in CA , polarized by a general base as in carboxypeptidase A to generate a nucleophile for catalysis or displaced by the substrate as in alkaline phosphatase; EC 3. In the zinc hydrolases and lyases, such as the zinc proteases and CAs, the zinc ion serves as a powerful electrophilic catalyst by providing all or a combination of the following: 1 an activated water molecule for nucleophilic attack, 2 polarization of the carbonyl of the scissile bond and 3 stabilization of the negative charge in the transition state Christianson and Cox, , Lovejoy et al.
The X-ray structures of catalytic zinc enzymes from four of the six classes of enzymes oxidoreductases, transferases, hydrolases and lyases have been determined, and they define the features of catalytic zinc-binding sites. Unlike the structural sites, the metal ion in catalytic sites is generally coordinated to the side chain of three amino acid residues, a combination of histidine, glutamate, aspartate and cysteine, and a solvent molecule completes the tetrahedral coordination sphere Table 1 for reviews, see Christianson , Jernigan et al.
However, the zinc polyhedra of adenosine deaminase EC 3. In catalytic zinc sites, histidine is the most frequently observed ligand, distantly followed by glutamic acid and then aspartic acid and cysteine. In non—coenzyme-dependent zinc enzymes, a short spacer with a rigid arrangement of one to three amino acids intervening between the first two ligands, L 1 and L 2 Table 1 , may constitute a nucleus for the zinc-binding site i. The third ligand, L 3 , is separated from L 2 by a longer spacer whose length varies greatly 5— amino acids and may be responsible for the spatial formation of the active site, allowing some flexibility to the coordination sphere.
The zinc-binding site of CA II. For these interactions, the metal ion prefers a head-on and in-plane approach to the sp 2 lone pair of the nitrogen atom Vedani and Huhta Scheme 3. Carboxylate-zinc interactions with syn-stereochemistry are observed more frequently than those with anti-stereochemistry, and the zinc ion displays a preference to be in the plane of the carboxyl Carrell et al. A stereochemical analysis of cysteine-zinc interactions in the Brookhaven Data Bank revealed that the average sulfur-zinc distance is 2.
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A feature common to all zinc sites is that the metal ion is surrounded by a shell of hydrophilic groups that is embedded within a larger shell of hydrophobic groups Yamashita et al. In addition, the amino acid side chains serving as zinc ligands in these structures often make hydrogen bond contacts with other residues, perhaps to preorder the metal ion binding site and lower the entropic cost of binding the metal ion Christianson These interactions between metal ion and ligand have been proposed to orient the metal ligands, enhance the electrostatic interaction between metal and ligand and modulate the zinc-water p K a Argos et al.
Interestingly, the catalytic metal in two zinc metalloproteins is believed to have a central role in regulation of enzyme activity. The first example is stromelysin EC 3. This activation involves the replacement of a thiolate zinc ligand with a water molecule, yielding the catalytically active His 3 H 2 O zinc site Gooley et al. The tetrahedral Cys 4 zinc polyhedron in the N-terminal domain of Ada is important to stabilize the tertiary fold.
However, in addition, this zinc site catalyzes the direct, irreversible transfer of a methyl group from the S p diastereomer of DNA methylphosphotriester to the sulfur of Cys 69 in the coordination sphere Myers et al. This conversion of the thiolate metal ligand to a more weakly bound thioether ligand on methyl transfer has been proposed to propel structural changes that reveal the sequence-specific DNA binding conformation of the protein Myers et al. In this conformation, Ada functions as a transcription factor, inducing genes that confer resistance to methylating agents.
The proposed role of the zinc ion in Ada, coordinating the cysteine thiolate to lower the p K a and enhance the reactivity of this group Matthews and Goulding , Myers et al. This class of zinc metalloproteins may indicate a new catalytic function of the zinc ion: to enhance the nucleophilicity of a thiol group at neutral pH Hightower and Fierke , Matthews and Goulding In multimetal enzymes, the two or more zinc or other metal atoms may operate in concert to enhance catalysis.
A class of catalytic zinc sites, called cocatalytic zinc sites, has been defined in which two or more zinc atoms are in close proximity to one another Vallee and Auld a , b , b. This group of enzymes includes alkaline phosphatase with two zinc ions and one magnesium ion , phospholipase C three zinc ions , nuclease P1 EC 3. A representative structure phospholipase C is shown in Figure 2. The first zinc ion, designated as the catalytic zinc Zn 1 in Fig.
For phosphate ester hydrolyzing enzymes, the product phosphate interacts with all three metals, displacing the weak unusual ligands in the second and third zinc sites to facilitate catalysis Vallee and Auld b. Example of cocatalytic zinc site: phospholipase C Hough et al. In phospholipase C, as in nuclease P1, the backbone amino and carbonyl groups of N-terminal Trp 1 coordinate Zn 2. In structural zinc sites, the metal ion is coordinated by four amino acid side chains, usually in a tetrahedral geometry, so that solvent is excluded as an inner sphere ligand for reviews, see Vallee and Auld b , Vallee et al.
Cysteine is by far the ligand observed most frequently in these sites, with histidine also being present in many cases and aspartate being present in one case Lovejoy et al. In contrast to catalytic zinc sites, these sites contain no regular pattern of spacer length between the protein zinc ligands, and the ligands can be located on a flexible loop rather than in a rigid secondary structure.
The high stability constants of these tetradentate zinc complexes ensure both local and overall structural stability similar to that provided by disulfides Vallee and Auld b. This enables proteins containing structural zinc atoms to perform a wide range of functions. Humans require a daily intake of 15 mg to maintain normal zinc concentrations Bryce-Smith , and zinc is involved in a wide range of functions that are essential for both physical and mental health; zinc is important to physiological functions in the bone, kidney and brain Sly et al. Zinc deficiency can cause retardation, cessation of growth, impaired wound healing, hair loss or defects leading to reproductive failure.
Zinc supplementation has successfully been used as a treatment of many illnesses and disorders, including dwarfism, sexual immaturity, acrodermatitis enteropathica inflammation of the skin and the small intestine , anorexia nervosa and bulimia nervosa Bryce-Smith An improved understanding of catalytic zinc sites is vital to an improved understanding of the role of zinc in the whole organism. Furthermore, catalytic zinc sites provide convenient targets for drugs because a wide range of functional groups i. This has been exploited in the use of topical CA inhibitors to lower intraocular pressure in patients with glaucoma Lippa and may provide a route to the development of novel antibiotics by inhibition of key enzymes in the lipid A biosynthetic pathway Wyckoff et al.
The active site features that delineate the catalytic role of the zinc site have not yet been completely defined for any zinc metalloenzymes, although CA has been studied in the greatest detail Christianson and Fierke The de novo design of zinc sites using solely the geometry of structurally characterized sites Hellinga , Hellinga et al. CA is a ubiquitous zinc metalloenzyme that catalyzes the reversible hydration of carbon dioxide.
In mammals, more than seven isozymes have been identified, and the isozyme CA II has the highest specific activity Silverman and Lindskog , Silverman and Vincent Although additional CA isozymes and families have been discovered in recent years, the main features of the catalytic mechanism of the mammalian enzyme are retained Lindskog In the first step, zinc-bound hydroxide attacks the carbonyl carbon of CO 2 to form zinc-bound bicarbonate; bicarbonate is subsequently displaced with water by a ligand-exchange step.
This hydrophobic region is probably the substrate CO 2 binding site, as indicated by the structure of the complex of the enzyme with bicarbonate and formate Hakansson et al. Based on the crystal structure of the enzyme complexed with bisulfite, a catalytic mechanism has been proposed, involving a transient pentacoordinate zinc ion Fig. The zinc-liganding side chains H 94 , H 96 and H are shown as ball-and-stick models. Although the CAs from the seven known isozymes and across a wide variety of species show a high degree of homology, two CAs have been discovered that differ significantly from mammalian CA II: a CA from the archaeon Methanosarcina thermophila Kisker et al.
Although there is little primary sequence similarity between the three families, many of the important active site residues are conserved, and all three CA families contain zinc at the active site Bracey et al. The CA from M. The zinc-binding site is made up of His 81 and His from one monomer and His from the neighboring monomer along with a coordinated water. However, because sulfonamides inhibit plant-type CAs Pocker and Ng as they do in mammalian CAs, it is presumed that the zinc bound to the plant enzyme is also catalytic.
The determinants of metal affinity and catalysis in the zinc-binding site of CA have been investigated using the complementary techniques of molecular biology, enzymology and structural biology. These studies highlight the functional importance of the nature of the zinc ligands, the structure of the active site hydrogen bond networks and the hydrophobic residues surrounding the zinc site Huang et al.
In CA II, and probably in all catalytic zinc sites, the protein scaffolding modulates the chemical properties of the zinc ion and zinc-bound solvent. Specifically, the protein plays a critical role in lowering the p K a of zinc-bound water to 6. In addition, the affinity of sulfonamide inhibitors, in which the sulfonamide anionic nitrogen displaces the zinc-water to directly coordinate zinc Vidgren et al.
These data suggest that the neutral ligand field in CA is essential for high affinity coordination of anions and efficient catalysis of CO 2 hydration. To further test this hypothesis, two neutral amino acid substitutions, asparagine or glutamine, were substituted for the histidine zinc ligands. The slight increase in the p K a of zinc-bound water and the high affinity for sulfonamide inhibitors of these carboxamide CA II variants indicate that the positive charge on the zinc ion is crucial for stabilizing bound anions at the active site of CA II Lesburg et al.
Furthermore, in each case, the activity of the asparagine or glutamine substitution was higher than the respective aspartate or glutamate substitution, suggesting that the net positive charge at the active site is important for stabilizing the catalytic transition state. However, the activity of the CA II variants with carboxamide side chains coordinating zinc decreased compared with the wild-type His 3 metal polyhedron in each case.
The bulky histidine ligands especially H may play a role in disfavoring higher coordination numbers, and therefore stabilizing a low coordination number, for the active site zinc ion of native CA II. This decreased coordination number should both depress the p K a of zinc-bound solvent and increase its reactivity Bertini et al. Furthermore, the metal affinity of the variants with carboxamide ligands is significantly compromised Lesburg et al.
Taken together, these data indicate that the neutral histidine ligands of the zinc-binding site optimize the electrostatic environment of the active site to maintain high catalytic activity and high zinc affinity in CA II. This loss of zinc-binding affinity is not due to the total loss of a hydrogen bond; compensatory hydrogen bonds are formed to either water or alternative amino acid side chains Lesburg and Christianson , Xue et al.
In each case, the hydrogen bond to the direct ligand is weakened, due to either the entropic cost of sequestering a solvent molecule into the hydrophobic active site Fersht or the nonoptimal hydrogen bonding stereochemistry. The weakening of these hydrogen bonds should increase the mobility of the direct ligands, and hence the role of the indirect ligands is to preorganize the histidines for optimal zinc coordination and avidity. Wen Shan Yew,, Eric L.
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Computer simulation and analysis of the reaction pathway of triosephosphate isomerase. Thermodynamics and energy coupling in the bacteriorhodopsin photocycle. Biochemistry , 30 20 , Iain A. Murray, Ann Lewendon, John A. Williams, Paul M. Cullis, William V. Shaw, and Andrew G. Alternative binding modes for chloramphenicol and 1-substituted chloramphenicol analogs revealed by site-directed mutagenesis and x-ray crystallography of chloramphenicol acetyltransferase. Biochemistry , 30 15 , William A. Beard, James R. Appleman, Shaoming Huang, Tavner J.
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Structure and Function of an Enzyme
Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. Kinetic description of the reaction of an RNA substrate that forms a mismatch at the active site. Biochemistry , 29 44 , Kinetic description of the reaction of an RNA substrate complementary to the active site. Vernon E. Anderson and W. Phosphonate analog substrates for enolase.
Biochemistry , 29 46 , Anderson and Kenneth A. Kinetic and structural analysis of enzyme intermediates: lessons from EPSP synthase. Chemical Reviews , 90 7 , Elizabeth E. About these proceedings Introduction Enzymes perform the executive role in growth, energy conversion, and repair of a living organism. Each enzyme discovered in the long history of enzymology has revealed its own individuality. Even closely related members of a family differ in specificity, stability or regulatory properties. Despite these, at first sight overwhelming aspects of individuality, common factors of enzymic reactions have been recognized.
Enzymes are stereospecific catalysts even when a nonspecific process would yield the same product. This binding close to catalytically competent groups is related to the enormous speed of enzyme-catalyzed reactions. These aspects of enzyme catalysis are discussed in Session 1. Substrate must diffuse from solution space to the enzyme's surface. This process is influenced and can be greatly facilitated by certain electrostatic propterties of enzymes. The dynamic events during catalysis are studied by relaxation kinetics or NMR techniques.
Enzym catalysis enzyme enzymes receptor.