Zinc-thiolate intermediate in catalysis of methyl group transfer in Methanosarcina barkeri.

Methyl group transfer reactions are essential in methane-forming pathways in all methanogens. The involvement of zinc in catalysis of methyl group transfer was studied for the methyltransferase enzyme MT2-A important for methanogenesis in Methanosarcina barkeri growing on methylamines. Zinc was shown to be required for MT2-A activity and was tightly bound by the enzyme with an apparent stability constant of 10(13.7) at pH 7.2. Oxidation was a factor influencing activity and metal stoichiometry of purified MT2-A preparations. Methods were developed to produce inactive apo MT2-A and to restore full activity with stoichiometric reincorporation of Zn(2+). Reconstitution with Co(2+) yielded an enzyme with 16-fold higher specific activity. Cysteine thiolate coordination in Co(2+)-MT2-A was indicated by high absorptivity in the 300-400 nm charge transfer region, consistent with more than one thiolate ligand at the metal center. Approximate tetrahedral geometry was indicated by strong d-d transition absorbance centered at 622 nm. EXAFS analyses of Zn(2+)-MT2-A revealed 2S + 2N/O coordination with evidence for involvement of histidine. Interaction with the substrate CoM (2-mercaptoethanesulfonic acid) resulted in replacement of the second N/O group with S, indicating direct coordination of the CoM thiolate. UV-visible spectroscopy of Co(2+)-MT2-A in the presence of CoM also showed formation of an additional metal-thiolate bond. Binding of CoM over the range of pH 6.2-7.7 obeyed a model in which metal-thiolate formation occurs separately from H(+) release from the enzyme-substrate complex. Proton release to the solvent takes place from a group with apparent pK(a) of 6.4, and no evidence for metal-thiolate protonation was found. It was determined that substrate metal-thiolate bond formation occurs with a Delta G degrees ' of -6.7 kcal/mol and is a major thermodynamic driving force in the overall process of methyl group transfer.

Characterization of the metal receptor sites in Escherichia coli Zur, an ultrasensitive zinc(II) metalloregulatory protein.

The Escherichia coli Zur protein is a Fur homologue that regulates expression of Zn(II) uptake systems. The zinc-loaded form of Zur is proposed to bind DNA and repress transcription of the znuABC genes. Recent in vitro data indicate that the transcriptional activity of Zur is half-maximal when free Zn(II) concentrations are in the sub-femtomolar range, making it the most sensitive Zn(II) metalloregulatory protein reported to date. Previous results indicate that Zur binds at least one zinc; however, little else is known about Zn(II) binding. We have purified E. coli Zur to homogeneity and found that it has two Zn(II) binding sites per monomer with different coordination environments. Using Zn(II) binding assays, ICP-AES analysis, and Zn EXAFS analysis, we show that one zinc is tightly bound in an S(3)(N/O) coordination environment. Both Co(II) and Zn(II) were substituted into the second metal binding site and probed by EXAFS and UV-visible absorption spectroscopy. These studies indicate that Co(II) is bound in an S(N/O)(3) coordination environment with tetrahedral geometry. The Zn(II) EXAFS of Zn(2)Zur, which is consistent with the results for both sites, indicates an average coordination environment of S(2)(N/O)(2), presumably due to one S(N/O)(3) site and one S(3)(N/O) site. These studies reveal the coordination environments that confer such exceptional zinc sensitivity and may provide the foundation for understanding the molecular basis of metal ion selectivity. A comparison of the metal binding sites in Zur with its Fe(II)-sensing homologue Fur provides clues as to why these two proteins with similar structures respond to two very different metal ions.

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.

Characterization of the zinc sites in cobalamin-independent and cobalamin-dependent methionine synthase using zinc and selenium X-ray absorption spectroscopy.

X-ray absorption spectroscopy has been used to investigate binding of selenohomocysteine to cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthase enzymes of Escherichia coli. We have shown previously [Peariso et al. (1998) J. Am. Chem. Soc. 120, 8410-8416] that the Zn sites in both enzymes show an increase in the number of sulfur ligands when homocysteine binds. The present data provide direct evidence that this change is due to coordination of the substrate to the Zn. Addition of L-selenohomocysteine to either MetE or the N-terminal fragment of MetH, MetH(2-649), causes changes in the zinc X-ray absorption near-edge structure that are remarkably similar to those observed following the addition of L-homocysteine. Zinc EXAFS spectra show that the addition of L-selenohomocysteine changes the coordination environment of the zinc in MetE from 2S + 2(N/O) to 2S + 1(N/O) + 1Se and in MetH(2-649) from 3S + 1(N/O) to 3S + 1Se. The Zn-S, Zn-Se, and Se-S bond distances determined from the zinc and selenium EXAFS data indicate that the zinc sites in substrate-bound MetE and MetH(2-649) both have an approximately tetrahedral geometry. The selenium edge energy for selenohomocysteine shifts to higher energy when binding to either methionine synthase enzyme, suggesting that there is a slight decrease in the effective charge of the selenium. Increases in the Zn-Cys bond distances upon selenohomocysteine binding together with identical magnitudes of the shifts to higher energy in the Se XANES spectra of MetE and MetH(2-649) suggest that the Lewis acidity of the Zn sites in these enzymes appears the same to the substrate and is electronically buffered by the Zn-Cys interaction.

The McbB component of microcin B17 synthetase is a zinc metalloprotein.

The microcin B17 synthetase converts glycine, serine, and cysteine residues in a polypeptide precursor into oxazoles and thiazoles during the maturation of the Escherichia coli antibiotic Microcin B17. This multimeric enzyme is composed of three subunits (McbB, McbC, and McbD), and it employs both ATP and FMN as cofactors. The McbB subunit was purified as a fusion with the maltose-binding protein (MBP), and metal analysis revealed that this protein binds 0.91+/-0.17 zinc atoms. Upon incubation of MBP-McbB with excess zinc, the stoichiometry increased to two atoms of zinc bound, but metal binding to the second site resulted in a decrease in the heterocyclization activity when MBP-McbB was reconstituted with the other components of the synthetase. Apo-protein was prepared by using p-hydroxymercuriphenylsulfonic acid (PMPS), and loss of the metal caused a severe reduction in enzymatic activity. However, if dithiothreitol was added to the PMPS reactions within a few minutes, enzymatic activity was retained and MBP-McbB could be reconstituted with zinc. Spectroscopic analysis of the cobalt-containing protein and extended X-ray absorption fine structure analysis of the zinc-containing protein both provide evidence for a tetrathiolate coordination sphere. Site-directed mutants of MBP-McbB as well as the synthetase tagged with the calmodulin-binding peptide were constructed. Activity assays and metal analysis were used to determine which of the six cysteines in McbB are metal ligands. These results suggest that the zinc cofactor in McbB plays a structural role.

Characterization of the heme in human cystathionine beta-synthase by X-ray absorption and electron paramagnetic resonance spectroscopies.

Human cystathionine beta-synthase is one of two key enzymes involved in intracellular metabolism of homocysteine. It catalyzes a beta-replacement reaction in which the thiolate of homocysteine replaces the hydroxyl group of serine to give the product, cystathionine. The enzyme is unusual in its dependence on two cofactors: pyridoxal phosphate and heme. The requirement for pyridoxal phosphate is expected on the basis of the nature of the condensation reaction that is catalyzed; however the function of the heme in this protein is unknown. We have examined the spectroscopic properties of the heme in order to assign the axial ligands provided by the protein. The heme Soret peak of ferric cystathionine beta-synthase is at 428 nm and shifts to approximately 395 nm upon addition of the thiol chelator, mercuric chloride. This is indicative of 6-coordinate low-spin heme converting to a 5-coordinate high-spin heme. The enzyme as isolated exhibits a rhombic EPR signal with g values of 2.5, 2.3, and 1.86, which are similar to those of heme proteins and model complexes with imidazole/thiolate ligands. Mercuric chloride treatment of the enzyme results in conversion of the rhombic EPR signal to a g = 6 signal, consistent with formation of the high-spin ferric heme. The X-ray absorption data reveal that iron in ferric cystathionine beta-synthase is 6-coordinate, with 1 high-Z scatterer and 5 low-Z scatterers. This is consistent with the presence of 5 nitrogens and 1 sulfur ligand. Together, these data support assignment of the axial ligands as cysteinate and imidazole in ferric cystathionine beta-synthase.

A short Fe-Fe distance in peroxodiferric ferritin: control of Fe substrate versus cofactor decay?

The reaction of oxygen with protein diiron sites is important in bioorganic syntheses and biomineralization. An unusually short Fe-Fe distance of 2.53 angstroms was found in the diiron (mu-1,2 peroxodiferric) intermediate that forms in the early steps of ferritin biomineralization. This distance suggests the presence of a unique triply bridged structure. The Fe-Fe distances in the mu-1, 2 peroxodiferric complexes that were characterized previously are much longer (3.1 to 4.0 angstroms). The 2.53 angstrom Fe-Fe distance requires a small Fe-O-O angle (approximately 106 degrees to 107 degrees). This geometry should favor decay of the peroxodiferric complex by the release of H2O2 and mu-oxo or mu-hydroxo diferric biomineral precursors rather than by oxidation of the organic substrate. Geometrical differences may thus explain how diiron sites can function either as a substrate (in ferritin biomineralization) or as a cofactor (in O2 activation).

NMR characterization of substrate binding in the phthalate dioxygenase system.

The paramagnetic enhancements in the NMR relaxation rates for the fluorine in fluorophthalates have been used to determine the position of the phthalate with respect to the mononuclear metal ion in native and metal-substituted derivatives of phthalate dioxygenase (PDO). These studies show directly that the substrate interacts with the mononuclear metal of PDO and provide the first structural characterization of this interaction. With a molecular mass of 200 kDa, PDO is one of the largest proteins studied to date by paramagnetic NMR. Two paramagnetically broadened (19)F lines were observed for monofluorophthalates bound to CoPDO. This demonstrates that fluorophthalate binds to PDO with a handedness, i.e., with the fluorine label facing to the "right" or to the "left", relative to the hyperfine tensor of the Co(II). The relative affinities of the two orientations are slightly different, with a 2-fold and 5-fold excess of the preferred orientation for 4-fluorophthalate and 3-fluorophthalate, respectively. The longitudinal relaxation rate (T(1)) and transverse relaxation rate (T(2)) data give mutually consistent fluorine to cobalt distances. These results are consistent with approximate bilateral symmetry, with the Co to 3-fluorophthalate distances ( approximately 5.5 A) approximately 25% longer than the Co to 4-fluorophthalate distances ( approximately 4. 5 A). A detailed geometric model is derived from these data. This structural characterization of the mononuclear site provides a framework to develop hypotheses for the mechanism of oxygenation by the Fe(II)-containing aromatic dioxygenases.

Identification of the zinc ligands in cobalamin-independent methionine synthase (MetE) from Escherichia coli.

Cobalamin-independent methionine synthase (MetE) from Escherichia coli catalyzes the transfer of a methyl group from methyltetrahydrofolate to homocysteine to form tetrahydrofolate and methionine. It contains 1 equiv of zinc that is essential for its catalytic activity. Extended X-ray absorption fine structure analysis of the zinc-binding site has suggested tetrahedral coordination with two sulfur (cysteine) and one nitrogen or oxygen ligands provided by the enzyme and an exchangeable oxygen or nitrogen ligand that is replaced by the homocysteine thiol group in the enzyme-substrate complex [González, J. C., Peariso, K., Penner-Hahn, J. E., and Matthews, R. G. (1996) Biochemistry 35, 12228-34]. Sequence alignment of MetE homologues shows that His641, Cys643, and Cys726 are the only conserved residues. We report here the construction, expression, and purification of the His641Gln, Cys643Ser, and Cys726Ser mutants of MetE. Each mutant displays significantly impaired activity and contains less than 1 equiv of zinc upon purification. Furthermore, each mutant binds zinc with lower binding affinity (K(a) approximately 10(14) M(-)(1)) compared to the wild-type enzyme (K(a) > 10(16) M(-)(1)). All the MetE mutants are able to bind homocysteine. X-ray absorption spectroscopy analysis of the zinc-binding sites in the mutants indicates that the four-coordinate zinc site is preserved but that the ligand sets are changed. Our results demonstrate that Cys643 and Cys726 are two of the zinc ligands in MetE from E. coli and suggest that His641 is a third endogenous ligand. The effects of the mutations on the specific activities of the mutant proteins suggest that zinc and homocysteine binding alone are not sufficient for activity; the chemical nature of the ligands is also a determining factor for catalytic activity in agreement with model studies of the alkylation of zinc-thiolate complexes.

Extracting dynamic information from EXAFS: simultaneous analysis of multiple temperature-dependent data.

A new approach to the extraction of dynamic information from extended X-ray absorption fine-structure (EXAFS) spectra has been developed. With this method, a complete set of temperature-dependent spectra are fit simultaneously to one of a variety of pair-distribution functions. Distributions are calculated in r-space using the appropriate absorber-scatterer pair potential. The temperature-dependent EXAFS spectra are calculated by summing k-space models over a range of distances and angles weighted according to the relative contribution of each geometry to the distribution. This approach allows refinement of data using a full multiple-scattering analysis with only modest computational time.

Metal ion chaperone function of the soluble Cu(I) receptor Atx1.

Reactive and potentially toxic cofactors such as copper ions are imported into eukaryotic cells and incorporated into target proteins by unknown mechanisms. Atx1, a prototypical copper chaperone protein from yeast, has now been shown to act as a soluble cytoplasmic copper(I) receptor that can adopt either a two- or three-coordinate metal center in the active site. Atx1 also associated directly with the Atx1-like cytosolic domains of Ccc2, a vesicular protein defined in genetic studies as a member of the copper-trafficking pathway. The unusual structure and dynamics of Atx1 suggest a copper exchange function for this protein and related domains in the Menkes and Wilson disease proteins.

EXAFS comparison of the dimanganese core structures of manganese catalase, arginase, and manganese-substituted ribonucleotide reductase and hemerythrin.

The solution structures of the binuclear Mn centers in arginase, Mn catalase, and the Mn-substituted forms of the Fe enzymes ribonucleotide reductase and hemerythrin have been determined using X-ray absorption spectroscopy (XAS). X-ray absorption near edge structure (XANES) spectra for these proteins were compared to those obtained for Mn(II) models. The Mn model spectra show an inverse correlation between the XANES peak maximum and the root-mean-square (RMS) deviation in metal-ligand bond lengths. For these complexes, the XANES maxima appear to be more effective than the 1s --> 3d areas as an indicator of metal-site symmetry. Arginase and Mn-substituted ribonucleotide reductase have symmetric nearest neighbor environments with low RMS deviation in bond length, while Mn catalase and Mn-substituted hemerythrin appear to have a larger RMS bond length deviation. The 1s --> 3d areas for arginase and Mn-substituted ribonucleotide reductase are consistent with six coordinate Mn, while the 1s --> 3d areas for Mn catalase and Mn-substituted hemerythrin are larger, suggesting that one or both of the Mn ions are five-coordinate in these proteins. Extended x-ray absorption fine structure (EXAFS) spectra were used to determine the Mn2 core structure for the four proteins. In order to quantitate the number of histidine residues bound to the Mn2 centers, EXAFS data for the crystallographically characterized model hexakis-imidazole Mn(II) dichloride tetrahydrate were used to calibrate the Mn-imidazole multiple scattering interactions. These calibrated parameters allowed the outer shell EXAFS to be fit to give a lower limit on the number of bound histidine residues. The EXAFS spectra for Mn-substituted ribonucleotide reductase and arginase are nearly identical, with symmetric Mn-nearest neighbor environments and outer shell scattering consistent with a lower limit of one histidine per Mn2 core. In contrast, the EXAFS data for Mn catalase and Mn-substituted hemerythrin show two distinct Mn-nearest neighbor shells, modeled as Mn-O at ca. 2.1 A and Mn-N at ca. 2.3 A, and outer shell carbon scattering consistent with a lower limit of ca. 2-3 His residues per Mn2 core. Only Mn catalase shows clear evidence for Mn...Mn scattering. The observed Mn...Mn distance is 3.53 A, which is significantly longer than the approximately 3.3 A distances that are typically observed for Mn(II)2 cores with two single atom bridges, but which is typical of the distances seen in Mn(II)2 cores having one single atom bridge (e.g., aqua or hydroxo) together with one or two carboxylate bridges. The absence of EXAFS-detectable Mn...Mn interactions for the other three proteins suggests either that there are no single atom bridges in these cases or that the Mn...Mn interactions are more disordered.

Cobalamin-independent methionine synthase from Escherichia coli: a zinc metalloenzyme.

Cobalamin-independent methionine synthase (MetE) from Escherichia coli catalyzes the transfer of a methyl group from methyltetrahydrofolate to homocysteine. Previous work had shown the existence of a reactive thiol group, cysteine 726, whose alkylation led to loss of all detectable enzymatic activity [González, J.C., et al. (1992) Biochemistry 31, 6045-6056]. A site-directed mutation of MetE, Cys726Ser, was constructed to investigate the possible role of this cysteine. The Cys726Ser protein was purified to homogeneity, affording a protein with no detectable activity. To assess the possibility that cysteine726 functions as a metal ligand, inductively coupled plasma-atomic emission spectrometry was performed. The wild-type enzyme contains 1.02 equiv of zinc per subunit; the Cys726Ser mutant does not contain zinc, supporting the view that cysteine726 is required for metal binding. A loss of enzymatic activity is observed upon removal of zinc from the wild-type MetE by incubation in urea and EDTA; activity can subsequently be restored by zinc reconstitution, suggesting that zinc is required for catalysis. Circular dichroism measurements further suggest that there are no major differences in the secondary structures of the wild-type and the Cys726Ser mutant enzymes. Extended X-ray absorption fine structure analysis has established that the average zinc environment is different in the presence of homocysteine than in its absence and is consistent with the changes expected for displacement of an oxygen or nitrogen ligand by the sulfur of homocysteine. A possible model for zinc-dependent activation of homocysteine by MetE is presented.

X-ray absorption spectroscopy of the zinc site in tRNA-guanine transglycosylase from Escherichia coli.

A key step in the post-transcriptional modification of tRNA with queuine in Escherichia coli is the exchange of the queuine precursor, preQ1 into tRNA. This reaction is catalyzed by tRNA-guanine transglycosylase (TGT). We have previously shown that the E. coli TGT is a zinc metalloprotein [Chong et al. (1995) Biochemistry 34, 3694-3701]. Site-directed mutagenesis studies indicated that cysteines 302, 304, 307 and histidine 317 constitute the four ligands to the zinc. The involvement of histidine 317 is somewhat confounded by the presence of histidine 316. We have examined the zinc site in TGT (wt) and TGT (H317C) by X-ray absorption spectroscopy. The TGT (wt) data are most consistent with a tetracoordinate zinc with one nitrogen and three sulfur ligands. Interestingly, the data for TGT (H317C) are also consistent with a tetracoordinate zinc with one nitrogen and three sulfur ligands. The outer shell imidazole scattering for TGT (H317C) appears to be somewhat more ordered than that for TGT (wt), consistent with our previous suggestion that the wild-type enzyme may exist in two conformations the predominant one involving histidine 317 liganding to the zinc and the minor conformer involving histidine 316 liganding to the zinc. The minor conformer, with histidine 316 coordinating the zinc, appears to have an overall conformation that is subtly different from that of the wild-type enzyme. While TGT (H317C) has kinetic parameters very similar to the wild-type, it does not form the homotrimer quaternary structure of the wild-type. TGT (H317A) has previously [Chong et al. (1995) Biochemistry 34, 3694-3701] been found to contain a significant amount of zinc, but is essentially inactive. This suggests that careful analysis of EXAFS data can reveal subtle conformational changes in metal binding sites that are not observed in more common probes of protein conformation such as CD spectroscopy.

Mechanism of manganese catalase peroxide disproportionation: determination of manganese oxidation states during turnover.

X-ray absorption near-edge structure (XANES) spectroscopy has been used to determine the oxidation state composition of the Mn site in Mn catalase under turnover conditions. The XANES data are consistent with parallel assignments based on electron paramagnetic resonance (EPR). However, a major advantage of the XANES assignments is that they permit the direct determination of the average oxidation states for derivatives that are EPR silent. In agreement with earlier work [Khangulov, S. V., Barynin, V. V., & Antonyuk-Barynina, S. V. (1990) Biochim. Biophys. Acta 1020, 25-33], these data show that the binuclear Mn site is reduced to Mn(II)/Mn(II) when peroxide is added in the presence of halide inhibitors. In addition, the present data provide the first direct evidence that the reduced enzyme is oxidized if peroxide is added in the absence of inhibitors. Under turnover conditions, the enzyme contains approximately a 2:1 ratio of Mn(II) and Mn(III). Similar results are obtained following incubation with dioxygen. These results are consistent with a Mn(II)/Mn(II)<==>Mn(III)/Mn(III) catalytic cycle and demonstrate that halide inhibition involves trapping the enzyme in the reduced state.

X-ray absorption spectroscopy of the iron site in Escherichia coli Fe(III) superoxide dismutase.

The local structure of the iron site in ferric superoxide dismutase from Escherichia coli has been characterized by X-ray absorption spectroscopy. In the resting state of the enzyme at pH 7.0, the iron is five-coordinate with an average metal-ligand bond length of 1.98 A. Binding of azide causes a reduction in the intensity of the bound state 1s-->3d transition and an increase of 0.08 A in average bond length. Both are indicative of an increase in the iron coordination number. Raising the pH from 7.0 to 10.5 causes a similar 0.08 A increase in the average bond length, again suggesting an increase in the iron coordination number. At intermediate pH (9.4), the average bond length is 2.03 A, consistent with an approximately 50:50 mixture of the limiting high and low pH forms. Similarly, the absorption edge structure varies continuously from pH 7 to 10.5. These spectra can be fit to a titration curve with a pKa of approximately 9.8. These data suggest that the pH-dependent transition, previously identified by UV-vis, EPR, and activity measurements, may be the conversion of the iron from five- to six-coordinate, presumably through coordination by hydroxide. The 1s-->3d transition for ferric superoxide dismutase at high pH is broader but not significantly less intense than that at pH 7. This suggests that the high pH form may be significantly distorted from octahedral symmetry. At pH 7, the ferric and ferric + azide samples undergo slow X-ray induced photoreduction.(ABSTRACT TRUNCATED AT 250 WORDS)

Thiol ligation of two zinc atoms to a class I tRNA synthetase: evidence for unshared thiols and role in amino acid binding and utilization.

Class I tRNA synthetases generally contain a characteristic N-terminal catalytic core joined to a C-terminal domain that is idiosyncratic to the enzyme. The closely related class I Escherichia coli methionyl- and isoleucyl-tRNA synthetases each have a single zinc atom coordinated to ligands contained in the catalytic domain. Isoleucyl-tRNA synthetase has a second, functionally essential, zinc bound to ligands at the C-terminal end of the 939 amino acid polypeptide. Recent evidence suggested that this structure curls back and interacts directly or indirectly with the active site. We show here by X-ray absorption spectroscopy that the average Zn environment contains predominantly sulfur ligands with a Zn-S distance of 2.33 A. A model with eight coordinated thiolates divided between two Zn(Cys)4 structures best fit the data which are not consistent with a thiolate-bridged Zn2(Cys)6 structure joining the C-terminal end with the N-terminal active site domain. We also show that zinc bound to the N-terminal catalytic core is important specifically for amino acid binding and utilization, although a direct interaction with zinc is unlikely. We suggest that, in addition to idiosyncratic sequences for tRNA acceptor helix interactions incorporated into the class-defining catalytic domain common to class I enzymes, the architecture of at least some parts of the amino acid binding sites may differ from enzyme to enzyme and include motifs that bind zinc.

Structural characterization of the copper site in galactose oxidase using X-ray absorption spectroscopy.

X-ray absorption spectroscopy has been used to characterize the local structural environment of the Cu ion in the reductively inactivated, oxidatively activated, and active+substrate oxidation state derivatives of galactose oxidase. In all three cases, the local environment of the Cu is best modeled by a single shell of low-Z (N or O) scatterers. This is generally consistent with the structure determined crystallographically, although the EXAFS bond lengths are slightly, but significantly, shorter than those found crystallographically. The best-fit average bond lengths are 1.97, 1.95, and 1.98 A for inactive, active, and active+substrate, respectively. The CuII ion in the active and inactive derivatives has an apparent coordination number of 4, consistent with the equatorial ligation seen crystallographically. The CuI ion in the reduced+substrate derivative appears to have either a lower coordination number or a significantly more distorted local environment. The observed CuI-(N/O) bond length favors a model where the Cu become 3-coordinate in the substrate-reduced complex.