Metal-coordination sphere in the methylated Ada protein-DNA co-complex

Crystal structures of cobalamin-independent methionine synthase (MetE) from Streptococcus mutans: a dynamic zinc-inversion model

Cobalamin-independent methionine synthase (MetE) catalyzes the direct transfer of a methyl group from methyltetrahydrofolate to l-homocysteine to form methionine. Previous studies have shown that the MetE active site coordinates a zinc atom, which is thought to act as a Lewis acid and plays a role in the activation of thiol. Extended X-ray absorption fine structure studies and mutagenesis experiments identified the zinc-binding site in MetE from Escherichia coli. Further structural investigations of MetE from Thermotoga maritima lead to the proposition of two models: "induced fit" and "dynamic equilibrium", to account for the catalytic mechanisms of MetE. Here, we present crystal structures of oxidized and zinc-replete MetE from Streptococcus mutans at the physiological pH. The structures reveal that zinc is mobile in the active center and has the possibility to invert even in the absence of homocysteine. These structures provide evidence for the dynamic equilibrium model.

DNA recognition by the DNA primase of bacteriophage T7: a structure-function study of the zinc-binding domain

Synthesis of oligoribonucleotide primers for lagging-strand DNA synthesis in the DNA replication system of bacteriophage T7 is catalyzed by the primase domain of the gene 4 helicase-primase. The primase consists of a zinc-binding domain (ZBD) and an RNA polymerase (RPD) domain. The ZBD is responsible for recognition of a specific sequence in the ssDNA template whereas catalytic activity resides in the RPD. The ZBD contains a zinc ion coordinated with four cysteine residues. We have examined the ligation state of the zinc ion by X-ray absorption spectroscopy and biochemical analysis of genetically altered primases. The ZBD of primase engaged in catalysis exhibits considerable asymmetry in coordination to zinc, as evidenced by a gradual increase in electron density of the zinc together with elongation of the zinc-sulfur bonds. Both wild-type primase and primase reconstituted from purified ZBD and RPD have a similar electronic change in the level of the zinc ion as well as the configuration of the ZBD. Single amino acid replacements in the ZBD (H33A and C36S) result in the loss of both zinc binding and its structural integrity. Thus the zinc in the ZBD may act as a charge modulation indicator for the surrounding sulfur atoms necessary for recognition of specific DNA sequences.

Metal active site elasticity linked to activation of homocysteine in methionine synthases

Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.

Catalysis of methyl group transfers involving tetrahydrofolate and B(12)

This review focuses on the reaction mechanism of enzymes that use B(12) and tetrahydrofolate (THF) to catalyze methyl group transfers. It also covers the related reactions that use B(12) and tetrahydromethanopterin (THMPT), which is a THF analog used by archaea. In the past decade, our understanding of the mechanisms of these enzymes has increased greatly because the crystal structures for three classes of B(12)-dependent methyltransferases have become available and because biophysical and kinetic studies have elucidated the intermediates involved in catalysis. These steps include binding of the cofactors and substrates, activation of the methyl donors and acceptors, the methyl transfer reaction itself, and product dissociation. Activation of the methyl donor in one class of methyltransferases is achieved by an unexpected proton transfer mechanism. The cobalt (Co) ion within the B(12) macrocycle must be in the Co(I) oxidation state to serve as a nucleophile in the methyl transfer reaction. Recent studies have uncovered important principles that control how this highly reducing active state of B(12) is generated and maintained.

Modeling the Metal Center of Cys4 Zinc Proteins

We present here a 67Zn solid-state NMR investigation of several model complexes of zinc coordinated by four sulfurs. The lineshapes were obtained at a variety of magnetic fields from 11.7 T (500 MHz for 1H) to 21.15 T (900 MHz for 1H) and at ambient temperature down to 10 K. The quadrupole coupling constants, Cq's, ranged from 3.25 to 16.7 MHz throughout the series, while the average bond distances only spanned 2.34-2.36 A. Reasonable agreement with experiment was achieved in the molecular orbital calculations using DFT methods and the local density approximation to predict electric field gradients.

Cobalamin-independent methionine synthase (MetE): a face-to-face double barrel that evolved by gene duplication

Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two (βα)₈ barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys)₃Zn site in the related enzymes, MetH and betaine–homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E·Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer.

By solving the structure of MetE, the authors have shed light on how the chemically difficult transfer of a methyl group from methyltetrahydrofolate to homocysteine can occur

Electronic Structure Control of the Nucleophilicity of Transition Metal−Thiolate Complexes: An Experimental and Theoretical Study

New metal(II)-thiolate complexes supported by the tetradentate ligand 1,5-bis(2-pyridylmethyl)-1,5-diazacyclooctane (L(8)py(2)) have been synthesized and subjected to physical, spectroscopic, structural, and computational characterization. The X-ray crystal structures of these complexes, [L(8)py(2)M(S-C(6)H(4)-p-CH(3))]BPh(4) (M = Co, Ni, Zn), reveal distorted square-pyramidal divalent metal ions with four equatorial nitrogen donors from L(8)py(2) and axial p-toluenethiolate ligands. The reactions of the complexes with benzyl bromide produce isolable metal(II)-bromide complexes (in the cases of Co and Ni) and the thioether benzyl-p-tolylsulfide. This reaction is characterized by a second-order rate law (nu = k(2)[L(8)py(2)M(SAr)(+)][PhCH(2)Br]) for all complexes (where M = Fe, Co, Ni, or Zn). Of particular significance is the disparity between k(2) for M = Fe and Co versus k(2) for M = Ni and Zn, in that k(2) for M = Ni and Zn is ca. 10 times larger (faster) than k(2) for M = Fe and Co. An Eyring analysis of k(2) for [L(8)py(2)Co(SAr)](+) and [L(8)py(2)Ni(SAr)](+) reveals that the reaction rate differences are not rooted in a change in mechanism, as the reactions of these complexes with benzyl bromide exhibit comparable activation parameters (M = Co: DeltaH() = 45(2) kJ mol(-)(1), DeltaS() = -144(6) J mol(-)(1) K(-)(1); M = Ni: DeltaH() = 43(3) kJ mol(-)(1), DeltaS() = -134(8) J mol(-)(1) K(-)(1)). Electronic structure calculations using density functional theory (DFT) reveal that the enhanced reaction rate for [L(8)py(2)Ni(SAr)](+) is rooted in a four-electron repulsion (or a "filled/filled interaction") between a completely filled nickel(II) d(pi) orbital and one of the two thiolate frontier orbitals, a condition that is absent in the Fe(II) and Co(II) complexes. The comparable reactivity of [L(8)py(2)Zn(SAr)](+) relative to that of [L(8)py(2)Ni(SAr)](+) arises from a highly ionic zinc(II)-thiolate bond that enhances the negative charge density on the thiolate sulfur. DFT calculations on putative thioether-coordinated intermediates reveal that the Co(II)- and Zn(II)-thioethers exhibit weaker M-S bonding than Ni(II). These combined results suggest that while Ni(II) may serve as a competent replacement for Zn(II) in alkyl group transfer enzymes, turnover may be limited by slow product release from the Ni(II) center.

Vanadium suppresses sister-chromatid exchange and DNA-protein crosslink formation and restores antioxidant status and hepatocellular architecture during 2-acetylaminofluorene-induced experimental rat hepatocarcinogenesis

Vanadium is an important regulator of cellular growth, differentiation, and cell death, and thus has received increasing attention to be an effective cancer chemopreventive agent. In the present study, attempts have been made to investigate the in vivo antineoplastic effect of this micronutrient at the 0.5 ppm dosage in drinking water, by monitoring hepatic nodulogenesis and hepatocellular phenotype followed by antioxidant status and atomic absorption spectrometric estimation of some essential biometals during the multistage of carcinogenesis induced by 2-acetylaminofluorene (2-AAF; 0.05% in basal diet). Finally, sister-chromatid exchange (SCE) and DNA-protein crosslink (DPC) formation, as potential biomarkers were estimated to find out the suppressive effect of vanadium at the molecular level. The results showed that vanadium administration throughout the experiment reduced the relative liver weight, nodular incidence (48.40%), total number, and multiplicity (63.91%), and altered the size of visible persistent nodules (PNs) with concurrent restoration of hepatic glutathione (P < 0.01), glutathione-S-transferase (P < 0.001) and manganese-dependent superoxide dismutase (P < 0.001) activities as well as, hepatic zinc and copper contents (P < 0.001) when compared to the carcinogen control. Moreover, vanadium treatment significantly reduced SCE frequency (50.24%) and DPC coefficient (P < 0.001; 21.30%). Our results, thus, strongly suggest that supplementary vanadium at a dose of 0.5 ppm, when administered continuously throughout the study, than administered either in the initiation or promotion phase alone, is very much effective in suppressing neoplastic transformation during 2-AAF-induced in vivo rat hepatocarcinogenesis.

SpaC and NisC, the Cyclases Involved in Subtilin and Nisin Biosynthesis, Are Zinc Proteins

Lantibiotics are peptide-derived antimicrobial agents that are ribosomally synthesized and posttranslationally modified by a multienzyme complex to their biologically active forms. Nisin has attracted much attention recently due to its novel mechanism of action including specific binding to the bacterial cell wall precursor lipid II, followed by membrane permeabilization. Nisin has been commercially used as a food preservative, while other lantibiotics show promising activity against bacterial infections. The posttranslational modifications are believed to be carried out by a multienzyme complex. At present the enzymes catalyzing the formation of the lantibiotic signature structural motifs, dehydroalanine (Dha), dehydrobutyrine (Dhb), lanthionine (Ln), and methyllanthionine (MeLn), are poorly characterized. In an effort to gain insight into the mechanism by which lantibiotics are biosynthesized, the cyclase enzymes involved in the synthesis of nisin and subtilin (NisC and SpaC, respectively) have been cloned, expressed, and purified. Both proteins exist as monomers in solution and contain a stoichiometric zinc atom. EXAFS data on SpaC and a C349A mutant are in line with two cysteine ligands to the metal in the wild-type enzyme with possibly two additional histidines. The two cysteine ligands are likely Cys303 and Cys349 on the basis of sequence alignments and EXAFS data. The metal may function to activate the cysteine thiol of the peptide substrate toward intramolecular Michael addition to the dehydroalanine and dehydrobutyrine residues in the peptide.

Betaine-homocysteine methyltransferase: zinc in a distorted barrel

Betaine-homocysteine methyl transferase (BHMT) catalyzes the synthesis of methionine from betaine and homocysteine (Hcy), utilizing a zinc ion to activate Hcy. BHMT is a key liver enzyme that is important for homocysteine homeostasis. X-ray structures of human BHMT in its oxidized (Zn-free) and reduced (Zn-replete) forms, the latter in complex with the bisubstrate analog, S(delta-carboxybutyl)-L-homocysteine, were determined at resolutions of 2.15 A and 2.05 A. BHMT is a (beta/alpha)(8) barrel that is distorted to construct the substrate and metal binding sites. The zinc binding sequences G-V/L-N-C and G-G-C-C are at the C termini of strands beta6 and beta8. Oxidation to the Cys217-Cys299 disulfide and expulsion of Zn are accompanied by local rearrangements. The structures identify Hcy binding fingerprints and provide a prototype for the homocysteine S-methyltransferase family.

Advances in the structure and chemistry of metallothioneins

A low molecular weight (6-7 kDa) class of metalloproteins, designated as metallothioneins (MTs), exhibit repeated sequence motifs of either CxC or CxxC through which mono or divalent d(10) metal ions are bound in polymetallic-thiolate clusters. The preservation of metal-thiolate clusters in an increasing number of three-dimensional structures of these proteins signifies the importance of this structural motif. This review focuses on the recent developments regarding the versatile and striking chemical reactivity of MTs as well as on the existence of conformational/configurational dynamics within their structure. Both properties and their interplay are likely to be essential for the still elusive biological function of these proteins.

Chemical communication across the zinc tetrathiolate cluster in Escherichia coli Ada, a metalloactivated DNA repair protein

The Escherichia coli Ada protein repairs methylphosphotriesters in DNA through direct, irreversible transfer to a cysteine residue on the protein, Cys 69. Methylation of Cys 69 increases the sequence-specific DNA-binding activity of Ada by 10(3)-fold, enabling the methylated protein to activate transcription of a methylation-resistance regulon. The thiolate sulfur atom of Cys 69 is coordinated to a tightly bound zinc ion in the Ada N-terminal domain, and this metal-ligand interaction plays a direct role in promoting the DNA repair chemistry. Ada is thus the founding member of a mechanistic class of proteins that employ metalloactivated thiolates as nucleophiles, other examples of which include protein prenyltransferases and cobalamin-independent methionine synthase. Here we have probed the role of the three other Cys residues in Ada that together with Cys 69 coordinate the zinc through mutation to the alternative ligand residues Asp and His. All of the mutant proteins folded properly and bound zinc, but none of them exhibited measurable levels of DNA repair activity. Significantly, the Cys-to-His mutant proteins retained nearly wild-type sequence-specific DNA-binding activity in the unmethylated state. These findings demonstrate that the three "spectator" Cys ligands communicate chemically with Cys 69 through the bound metal ion.

Structural basis for the functional switch of the E. coli Ada protein

The Escherichia coli protein Ada specifically repairs the S(p) diastereomer of DNA methyl phosphotriesters in DNA by direct and irreversible transfer of the methyl group to its own Cys 69 which is part of a zinc-thiolate center. The methyl transfer converts Ada into a transcriptional activator that binds sequence-specifically to promoter regions of its own gene and other methylation resistance genes. Ada thus acts as a chemosensor to activate repair mechanisms in situations of methylation damage. Here we present a highly refined solution structure of the 10 kDa N-terminal domain, N-Ada10, which reveals structural details of the nonspecific DNA interaction of N-Ada10 during the repair process and provides a basis for understanding the mechanism of the conformational switch triggered by methyl transfer. To further elucidate this, EXAFS (extended X-ray absorption fine structure) and XANES (X-ray absorption near-edge structure) data were acquired, which confirmed that the zinc-thiolate center is maintained when N-Ada is methylated. Thus, ligand exchange is not the mechanism that enhances sequence-specific DNA binding and transcriptional activation upon methylation of N-Ada. The mechanism of the switch was further elucidated by recording NOESY spectra of specifically labeled methylated-Ada/DNA complexes, which showed that the transferred methyl group makes many contacts within N-Ada but none with the DNA. This implies that methylation of N-Ada induces a structural change, which enhances the promoter affinity of a remodeled surface region that does not include the transferred methyl group.

Mechanistic studies of rat protein farnesyltransferase indicate an associative transition state

Protein farnesyltransferase is a zinc metalloenzyme that catalyzes the transfer of a 15-carbon farnesyl group to a conserved cysteine residue of a protein substrate. Both electrophilic and nucleophilic mechanisms have been proposed for this enzyme. In this work, we investigate the detailed catalytic mechanism of mammalian protein farnesyltransferase by measuring the effect of metal substitution and/or substrate alterations on the rate constant of the chemical step. Substitution of cadmium for the active site zinc enhances peptide affinity approximately 5-fold and decreases the rate constant for the formation of the thioether product approximately 6-fold, indicating changes in the metal-thiolate coordination in the catalytic transition state. In addition, the observed rate constant for product formation decreases for C3 fluoromethyl farnesyl pyrophosphate substrates, paralleling the number of fluorines at the C3 methyl position and indicating that a rate-contributing transition state has carbocation character. Magnesium ions do not affect the affinity of either the peptide or the isoprenoid substrate but specifically enhance the observed rate constant for product formation 700-fold, suggesting that magnesium coordinates and activates the diphosphate leaving group. These data suggest that FTase catalyzes protein farnesylation by an associative mechanism with an "exploded" transition state where the metal-bound peptide/protein sulfur has a partial negative charge, the C1 of FPP has a partial positive charge, and the bridge oxygen between C1 and the alpha phosphate of FPP has a partial negative charge. This proposed transition state suggests that stabilization of the developing charge on the carbocation and pyrophosphate oxygens is an important catalytic feature.

Methylation of Iron-Sulfur Complexes by Trimethyl Phosphate

Reaction of [(C(4)H(9))(4)N](2)[Fe(4)S(4)(SR)(4)] (R = C(6)H(5), C(2)H(5)) with (CH(3)O)(3)PO in DMSO-d(6) afforded [(C(4)H(9))N](2){Fe(4)S(4)(SR)(3)[(CH(3)O)(2)PO(2)]} and CH(3)SR as revealed by (1)H and (31)P{(1)H} NMR spectroscopy. The more reduced species [(C(2)H(5))(4)N](3)[Fe(4)S(4)(SC(2)H(5))(4)] gave uncoordinated (CH(3)O)(2)PO(2)(-) and CH(3)SC(2)H(5) in addition to an unidentified iron thiolate species. Stoichiometric methylation of mononuclear [(C(2)H(5))(4)N](2)[Fe(SC(2)H(5))(4)] by (CH(3)O)(3)PO afforded [Fe(2)(SC(2)H(5))(6)](2)(-) as well as free (CH(3)O)(2)PO(2)(-) and CH(3)SC(2)H(5). Kinetic studies revealed the rate constant for methylation of [(C(2)H(5))(4)N](3)[Fe(4)S(4)(SC(2)H(5))(4)] to be more than 200-fold higher than that of the oxidized analogues [(C(4)H(9))(4)N](2)[Fe(4)S(4)(SR)(4)] (R = C(6)H(5), C(2)H(5)). The compound [(C(2)H(5))(4)N](2)[Fe(SC(2)H(5))(4)] had the highest rate constant, >/=5 x 10(-)(3) s(-)(1) at concentrations of 5.0 mM in complex and 1.0 mM in (CH(3)O)(3)PO. Attempts to prepare site-differentiated tetranuclear iron-sulfur complexes by removing one thiolate via methylation and addition of second, capping ligands are described. These results are discussed in the context of protein metal thiolate moieties that transfer methyl cations for substrate synthesis, such as carbon monoxide dehydrogenase/acetyl coenzyme A synthase, and repair of DNA alkylation damage.

Zinc-catalyzed sulfur alkyation:insights from protein farnesyltransferase

Zinc metalloenzymes catalyze many important cellular reactions. Recently, the involvement of zinc in the catalysis of alkylation of sulfur groups has gained prominence. Current studies of the zinc metalloenzyme protein farnesyltransferase have shed light on its structure and catalytic mechanism, as well as the general mechanism of zinc-catalyzed sulfur alkylation.

Methylation of Tethered Thiolates in [(bme-daco)Zn](2) and [(bme-daco)Cd](2) as a Model of Zinc Sulfur-Methylation Proteins

The dimeric dithiolate complex [1,5-bis(mercaptoethyl)-1,5-diazacyclooctanato]zinc(II), [(bme-daco)Zn](2) or Zn-1, and its cadmium analogue, Cd-1, were investigated as models for the active site of zinc-dependent methylation proteins. The key issue addressed was whether alkylation of a thiolate in a relatively rigid tetradentate ligand would result in coordination of the thioether product to the metal. On the basis of (1)H and (13)C NMR spectroscopy and similar reactivity toward alkylating agents, the newly synthesized cadmium complex, Cd-1, is proposed to be isostructural with the previously reported Zn-1 complex, which is known from X-ray crystallography to be dimeric in the solid state (Tuntulani, T.; Reibenspies, J. H.; Farmer, P. J.; Darensbourg, M. Y. Inorg. Chem.1992, 31, 3497). Iodomethane reacts with Zn-1 in hot CH(3)OH/CH(3)CN to produce a thioether which dissociates, replaced by coordination of iodide in the pseudotetrahedral complex, (Me(2)bme-daco)ZnI(2) or Zn-2. Complex Zn-2 crystallizes in the triclinic P&onemacr; space group with a = 7.911(2) Å, b = 10.675(2) Å, c = 12.394(2) Å, alpha = 75.270(10) degrees, beta = 75.270(10) degrees, gamma = 82.12(2) degrees, V = 998.270 Å(3), and Z = 2. An analogous reaction was observed for the cadmium derivative, Cd-1, which displays a (1)H NMR spectrum identical to that of Zn-2. In attempts to promote thioether binding, the iodide was displaced by addition of AgBF(4) to solutions of Zn-2 or the BF(4)(-) analogue was synthesized directly from Zn(BF(4))(2) and methylated ligand, Me(2)bme-daco, to yield Zn-3. Similar reactions with the cadmium analogue yielded a product identified as Cd-3 that was indistinguishable from Zn-3 by (1)H NMR. The (113)Cd NMR spectra of Cd-3 displayed a single resonance at 88 ppm consistent with a hard donor environment and inconsistent with sulfur binding. As a further attempt to induce thioether binding to zinc, the macrocyclization reagent 1,3-dibromopropane was added to Zn-1. The resulting product, [BrZn(macrocycle)](+), was only slightly soluble in pyridine and identified by +FAB/MS as the desired macrocyclic product with a large amount of free macrocycle ligand. Recrystallization from pyridine/ether resulted in loss of the zinc as Zn(py)(2)Br(2), which was obtained as colorless crystals and characterized by X-ray crystallography. Complex Zn(py)(2)Br(2) crystallizes in the monoclinic P2(1)/c space group with a = 8.534(2) Å, b = 18.316(4) Å, c = 8.461(2) Å, beta = 101.07(3) degrees, V = 1297.9(5) Å(3), and Z = 4.

Enzyme-catalyzed methyl transfers to thiols: the role of zinc

Zinc has been identified as a cofactor in a growing number of proteins that utilize thiols as nucleophiles, including proteins that catalyze the transfer of methyl groups to thiols. The latter category includes the Ada protein involved in the response of E. coli to DNA alkylation, cobalamin-independent and cobalamin-dependent methionine synthase, and enzymes involved in the formation of methylcoenzyme M in methanogenesis. Farnesyl-protein transferase and geranylgeranyl-protein transferase also contain zinc and an X-ray structure of farnesyl-protein transferase has recently been determined. Within the past year, studies on the role of zinc in these proteins and in model compounds have shown that the thiol substrates are coordinated to the zinc as thiolates, suggesting a role for zinc in maintenance of thiol reactivity at neutral pH.

Methyl Transfer to Mercury Thiolates: Effects of Coordination Number and Ligand Dissociation

The complexes [(CH(3))(4)N](2)[Hg(SC(6)H(5))(4)] and [(C(4)H(9))(4)N][Hg(SC(6)H(5))(3)] demethylate (CH(3)O)(3)PO as revealed by (1)H, (31)P{(1)H}, and (199)Hg{(1)H} NMR spectroscopy in DMSO-d(6) solution. The products of the [(CH(3))(4)N](2)[Hg(SC(6)H(5))(4)] reaction are CH(3)SC(6)H(5), (CH(3)O)(2)PO(2)(-), and [Hg(SC(6)H(5))(3)](-), whereas [Hg(SC(6)H(5))(3)](-) demethylates (CH(3)O)(3)PO to yield CH(3)SC(6)H(5) and {Hg(SC(6)H(5))(2)[(CH(3)O)(2)PO(2)]}(-). Kinetic and solution studies of [(CH(3))(4)N](2)[Hg(SC(6)H(5))(4)] reveal a rapid equilibrium between bound and free thiolate. The dissociated thiolate is the nucleophile active toward (CH(3)O)(3)PO. These results imply that the metal center of the inactive mercury derivative of the Escherichia coli Ada DNA alkylation repair protein may comprise a three-coordinate [Hg(S-cysteine)(3)](-) moiety and an unbound, protonated cysteine (HS-Cys69).

Alkyl Transfer to Metal Thiolates: Kinetics, Active Species Identification, and Relevance to the DNA Methyl Phosphotriester Repair Center of Escherichia coli Ada

The Ada protein of Escherichia coli employs a [Zn(S-cys)(4)](2)(-) site to repair deoxyribonucleic acid alkyl phosphotriester lesions. The alkyl group is transferred to a cysteine thiolate in a stoichiometric reaction. We describe a functional model for this chemistry in which a thiolate of [(CH(3))(4)N](2)[Zn(SC(6)H(5))(4)] accepts a methyl group from (CH(3)O)(3)PO. The thiolate salt (CH(3))(4)N(SC(6)H(5)) is also active in methyl transfer, but the thiol C(6)H(5)SH fails to react. Conductivity measurements and kinetic studies demonstrate that [(CH(3))(4)N](2)[Zn(SC(6)H(5))(4)] forms ion pairs in dimethyl sulfoxide (DMSO) solution (K(IP) = 13 +/- 4 M(-)(1)) which exhibit diminished reactivity. The reaction of [Zn(SC(6)H(5))(4)](2)(-) with (CH(3)O)(3)PO is first order with respect to each reagent. A second-order rate constant for this reaction, k(Zn), was determined to be (1.6 +/- 0.3) x 10(-)(2) M(-)(1) s(-)(1). From kinetic data and equilibria studies, all reactivity of [(CH(3))(4)N](2)[Zn(SC(6)H(5))(4)] toward (CH(3)O)(3)PO could be attributed to dissociated thiolate. Metal complexes representing alternative protein sites were prepared and displayed the following kinetic trend of methyl transfer ability: [(CH(3))(4)N](2)[Zn(SC(6)H(5))(4)] > [(CH(3))(4)N](2)[Co(SC(6)H(5))(4)] approximately [(CH(3))(4)N](2)[Cd(SC(6)H(5))(4)] > [(CH(3))(4)N][Zn(SC(6)H(5))(3)(MeIm)] > [Zn(SC(6)H(5))(2)(MeIm)(2)], where MeIm = 1-methylimidazole. These results are consistent with a dissociated thiolate being the active species and suggest that a similar mechanism might apply to alkyl phosphotriester repair by Ada.

Evidence for a catalytic role of zinc in protein farnesyltransferase. Spectroscopy of Co2+-farnesyltransferase indicates metal coordination of the substrate thiolate

Protein farnesyltransferase (FTase) is a zinc metalloenzyme that catalyzes the addition of a farnesyl isoprenoid to a conserved cysteine in peptide or protein substrates. We have substituted the essential Zn2+ in FTase with Co2+ to investigate the function of the metal polyhedron using optical absorption spectroscopy. The catalytic activity of FTase is unchanged by the substitution of cobalt for zinc. The absorption spectrum of Co2+-FTase displays a thiolate-Co2+ charge transfer band (epsilon320 = 1030 M(-1) cm(-1)) consistent with the coordination of one cysteine side chain and also ligand field bands (epsilon560 = 140 M(-1) cm(-1)) indicative of a pentacoordinate or distorted tetrahedral metal geometry. Most importantly, the ligand-metal charge transfer band displays an increased intensity (epsilon320 = 1830 M(-1) cm(-1)) in the ternary complex of FTase x isoprenoid x peptide substrate indicative of the formation of a second Co2+-thiolate bond as cobalt coordinates the thiolate of the peptide substrate. A similar increase in the ligand-metal charge transfer band in a product complex indicates that the sulfur atom of the farnesylated peptide also coordinates the metal. Transient kinetics demonstrate that thiolate-cobalt metal coordination also occurs in an active FTase x FPP x peptide substrate complex and that the rate constant for the chemical step is 17 s(-1). These data provide evidence that the zinc ion plays an important catalytic role in FTase, most likely by activation of the cysteine thiol of the protein substrate for nucleophilic attack on the isoprenoid.

Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR

The 10kDa amino-terminal fragment of Escherichia coli Ada protein (N-Ada10) repairs methyl phosphotriesters in DNA and possesses a tightly bound zinc ion. The complete resonance assignments of this protein domain have been obtained using multidimensional homonuclear and heteronuclear NMR experiments. The assignments served to study the internal mobility of this protein domain via 15N relaxation experiments. This involved the measurement of longitudinal and transverse 15N relaxation rates, as well as the amide proton solvent exchange rates. Relaxation rates in the rotating frame, R1 rho, of 15N nuclei were measured at different spin-lock field strengths, leading to the detection of two slow conformational exchange processes at Gly-25 and Gln-73. For the latter, which is next to the active site of this protein domain, the characteristic time of this process was found to be around 60 microseconds. The other relaxation experiments unveiled some regions of fast internal motions, faster than the overall correlation time. These motions were found in the N- and C- terminal tails, in segment 33-35 which forms the turn between beta-strands S1 and S2, and residues 47-52 located in a long loop preceding strand S3. The latter loop belongs to the potential DNA binding surface of N-Ada10. While the structure from residue 18 to residue 26 appears not well defined in the calculated structure, the relaxation experiments do not indicate higher mobility for this region. Residues at the N-terminal portion, including the first helix, the sequentially adjacent loop, and part of the second helix, exhibit internal motions close to the time scale of the overall rotational correlation time. This appears to be related to the fact that the first helix has no hydrogen bonds or salt bridges to the rest of the protein and is stabilized only by the involvement of some of its side chains in a hydrophobic core consisting of the side chains of two phenylalanines, a tryptophan, a leucine, and a valine. The four cysteines which bind the zinc show motions on different time scales ranging from microseconds to picoseconds. Thus the motions in the immediate region around the bound zinc of the DNA methyl phosphotriester repair domain are of relatively small amplitude but take place over a wide time range. On the other hand, high mobility is found in the turn connecting S1 and S2 and in the loop preceding S3, regions of the potential DNA binding surface.

Zinc binding in proteins and solution: a simple but accurate nonbonded representation

Force field parameters that use a combination of Lennard-Jones and electrostatic interactions are developed for divalent zinc and tested in solution and protein simulations. It is shown that the parameter set gives free energies of solution in good agreement with experiment. Molecular dynamics simulations of carboxypeptidase A and carbonic anhydrase are performed with these zinc parameters and the CHARMM 22 beta all-atom parameter set. The structural results are as accurate as those obtained in published simulations that use specifically bonded models for the zinc ion and the AMBER force field. The inclusion of longer-range electrostatic interactions by use of the Extended Electrostatics model is found to improve the equilibrium conformation of the active site It is concluded that the present parameter set, which permits different coordination geometries and ligand exchange for the zinc ion, can be employed effectively for both solution and protein simulations of zinc-containing systems.

Metal dependence of transcriptional switching in Escherichia coli Ada

The Escherichia coli Ada protein repairs methylphosphotriesters in DNA by direct, irreversible methyl transfer to one of its own cysteine residues. The methyl transfer process is autocatalyzed by coordination of the acceptor residue, Cys69, to a tightly bound zinc ion. Kinetic data reveal a 4-fold reduction in the methylphosphotriester repair activity for the Cd(II) form of Ada versus the native Zn(II)-bound form, thus confirming a direct role for the metal in autocatalysis. Quantitative electrophoretic mobility shift assays reveal that the specific DNA affinity of the protein is increased 10(3)-fold by transfer of a methyl group to Cys69; the Cd(II) and the Zn(II) forms of the protein behave similarly in this respect. This methylation-sensitive stimulation of binding underlies the ability of Ada to activate inducibly the transcription of a methylation-dependent regulon. We conclude that the chemical properties of the bound metal influence the transition state for autocatalytic methyl transfer, but not the structure that ultimately results from this process.

DNA repair proteins

DNA repair proteins act to correct mutagenic and toxic DNA damage, which can lead to cancer, aging and death. These proteins and their mechanisms of action have been found to be widely conserved between species, often from bacteria to man. Structural and biochemical studies on several bacterial enzymes involved in direct reversal and base excision repair have provided insights into the molecular basis of the recognition of damaged DNA and have also highlighted the novel roles that transition metals play in DNA repair.