Tetrahedral mercaptide complexes. Crystal and molecular structures of [(C6H5)4P]2M(SC6H5)4 complexes (M = cadmium(II), zinc(II), nickel(II), cobalt(II), and manganese(II))

Swenson, Dale C.; Baenziger, N. C.; Coucouvanis, D.

doi:10.1021/ja00474a053

Cited by 206 publications

(131 citation statements)

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“…Nevertheless, the Zn-S distances measured for ZnRd (Table 3) have a greater distortion along the 2-fold axis than the one found in the protein. Similar distortions were observed for several divalent metal ion complexes and were assigned to crystal packing forces (40). The synthetic analogues also displayed some heterogeneity in Zn-S bond length, but the trend was one shorter (2.329 A) bond and three longer (2.357 A, 2.362 A, and 2.363 A) ones, typical of trigonal pyramidal coordination (40), rather than two and two, as in Rd.…”

Section: Resultssupporting

confidence: 67%

Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.

Dauter

Wilson

Sieker

et al. 1996

Proc. Natl. Acad. Sci. U.S.A.

146

179

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The Zn(S,ys)4 unit is present in numerous proteins, where it assumes structural, regulatory, or catalytic roles. The same coordination is found naturally around iron in rubredoxins, several structures of which have been refined at resolutions of, or near to, 1 A. The fold of the small protein rubredoxin around its metal ion is an excellent model for many zinc finger proteins. Zn-substituted rubredoxin and its Fe-containing counterpart were both obtained as the products of the expression in Escherichia coli of the rubredoxinencoding gene from Clostridium pasteurianum. The structures of both proteins have been refined with an anisotropic model at atomic resolution (1.1 A, R = 8.3% for Fe-rubredoxin, and 1.2 A, R = 9.6% for Zn-rubredoxin) and are very similar. The most significant differences are increased lengths of the M-S bonds in Zn-rubredoxin (average length, 2.345 A) as compared with Fe-rubredoxin (average length, 2.262 A). An increase of the CA-CB-SG-M dihedral angles involving Cys-6 and Cys-39, the first cysteines of each of the Cys-Xaa-Xaa-Cys metal binding motifs, has been observed. Another consequence of the replacement of iron by zinc is that the region around residues 36-46 undergoes larger displacements than the remainder of the polypeptide chain. Despite these changes, the main features of the FeS4 site, namely a local 2-fold symmetry and the characteristic network of N-H... .S hydrogen bonds, are conserved in the ZnS4 site. The Zn-substituted rubredoxin provides the first precise structure of a Zn(S,ys)4 unit in a protein. The nearly identical fold of rubredoxin around iron or zinc suggests that at least in some of the sites where the metal has mainly a structural role-e.g., zinc fingers-the choice of the relevant metal may be directed by its cellular availability and mobilization processes rather than by its chemical nature.

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Section: Resultssupporting

confidence: 67%

Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.

Dauter

Wilson

Sieker

et al. 1996

Proc. Natl. Acad. Sci. U.S.A.

146

179

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“…The coordination of both pairs of zinc ions in horse liver alcohol dehydrogenase has been described as distorted tetrahedral in the X-ray crystallographic investigation at 0.24-nm resolution [18]. Only recently, tetrahedral low-molecular-weight complexes of transition metals with sulfur ligands have been synthesized and characterized [38,39,50]. In Table 3 various tetrahedral cobalt complexes with different numbers of sulfur and nitrogen ligands are compiled.…”

Section: Discussionmentioning

confidence: 99%

“…Here, models of both chromophores of cobalt alcohol dehydrogenases can be found. The noncatalytic site is paralleled by tetrathiophenolatocobaltate(I1) [39] and cobalt(1I)rubredoxin [51]. A model of the catalytic site in its binary complex with imidazole is represented by bis(2-mercapto-2,2-dimethylethylamino)cobaltate-(11) [38].…”

Section: Discussionmentioning

confidence: 99%

“…protein absorption). From the study of model compounds it can be inferred that the G and IZ components of the LMCT transitions between zinc and sulfur at 225 and 275 nm [38,39] and between cobalt and sulfur at 280 and 370 nm [38] contribute to the protein absorption. In fact, we observe different protein absorption maxima for the metallo-alcohol dehydrogenases.…”

Section: Spectral Properties Of the Various Cobalt Alcohol Dehydrogenmentioning

confidence: 99%

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Site‐Specific Substituted Cobalt(II) Horse Liver Alcohol Dehydrogenases

Maret

Anderson

Dietrich

et al. 1979

European Journal of Biochemistry

148

100

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The specific substitution, using highly selective techniques, of catalytic and/or noncatalytic zinc ions by cobaltous ions in horse liver alcohol dehydrogenase (EC 1 .I .1.1) has been studied with dissolved, crystalline and agarose-immobilised enzyme, in order to examine the effect of protein structure on the specificity of the metal exchange. The different binding sites can be clearly distinguished by the absorption spectra of their cobalt derivatives.In solution an anaerobic column chromatographic method made it possible to exchange half of the zinc in the enzyme by cobalt ions in a much shorter time than previous procedures. By raising the temperature in the exchange step, even the slowly exchanging zinc ions were substituted by cobalt, yielding products similar to cobalt alcohol dehydrogenases described earlier.Treatment of crystal suspensions of the enzyme with chelating agents (preferentially dipicolinic acid) gave an inactive protein with two zinc ions remaining bound. The enzyme could be reactivated by treatment of the crystalline protein with 5 mM zinc or cobaltous ions or by dialysis of dissolved inactive protein against 20 pM zinc or 1 mM cobaltous ions. Higher metal concentrations led to denaturation but the inactive protein could be crystallized from solution and then reactivated completely at higher metal concentrations. The preparation and absorption spectrum show that cobalt is bound specifically at the catalytic sites. Since metal substitution at these sites critically depends on the maintenance of the correct tertiary and quaternary structure, these must be preserved in the crystal lattice and partially altered in solution when the catalytic zinc ions are removed (or when excess of metal ions is applied), thus demonstrating the structure-stabilizing r61e of the catalytic metal ions.The enzyme immobilised on agarose, with unchanged content of active sites Eur. J . Biochem. 41, 475-4841, was treated like the crystal suspensions. Although half of the zinc was removed, some activity remained. After reactivation with cobaltous ions, a loss of about 30% active sites was measured. Thus the apparently homogeneous bound enzyme was rather heterogeneous in the properties of its catalytic metal binding sites. These results are taken as further proof for the dependence of the metal substitution on the proper tertiary and quaternary structure which is strained by multiple interactions in the covalently immobilised enzyme.Ahhreviations. Tes, 2-{ [tris(hydroxymethyl)methyl]amino}etha-nesulfonic acid; Tris: Tris(hydroxymethy1)-aminomethane; Mes, 2-(N-morpholino)ethanesulfonic acid. The differently substituted metallo-alcohol dehydrogenases are named as follows. The metal ions are differentiated as catalytic and noncatalytic by the characters (c) and (n) after the chemical symbol, i.e. Zn(c)zZn(n)~-enzyme = native enzyme; H4Zn(n)z-enzyme = enzyme depleted of the catalytic zinc ions; Zn(c)2Co(n)z-enzyme = enzyme substituted at the noncatalytic binding sites ('green hybrid' enzyme) ; CO(C)ZZn(n)2-enzyme = enzyme ...

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“…Synthetic compounds were synthesized as described in the literature (24)(25)(26)(27)(28)(29)(30). They were run as finely ground solids, which had been diluted with boron nitride and pressed into pellets of 1-mm thickness and which were supported by an Al spacer and enclosed by Mylar windows.…”

Section: Methodsmentioning

confidence: 99%

On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

Tan

Ensign

Ciurli

et al. 1992

Proc. Natl. Acad. Sci. U.S.A.

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The nickel/iron/sulfur center of the carbon monoxide dehydrogenase (carbon monoxide:(acceptor)oxidoreductase; EC 1.2.99.2) enzyme from Rhodospirillum rubrum (Rr-CODH) was studied by x-ray absorption spectroscopy at the Ni K edge. Extended x-ray absorption fine structure data show that the first Ni coordination shell consists of 2 S atoms at 2.23 A and 2-3 N/O atoms at 1.87 A. The edge structure indicates a distorted tetrahedral or five-coordinate Ni environment in both oxidized and reduced Rr-CODH. By comparing second-shell extended x-ray absorption fine structure data of Rr-CODH to that of (Et4N)3[NiFe3S4(SEt)4], a cubane-type cluster, it was clearly established that Ni in the Rr-CODH center is not involved in the core of a NiFe3S4 cubane cluster. One model consistent with the results is a mononuclear The metabolic pathways of certain bacteria involve conversion of CO to CO2 catalyzed by a Ni-containing enzyme, carbon monoxide dehydrogenase [CODH; carbon-monoxide: (acceptor)oxidoreductase; EC 1.2.99.2], now purified from several anaerobes (1-12). Some of these enzymes effect the synthesis of acetyl coenzyme A by means of the Wood pathway (13,14). Recent extended x-ray absorption fine structure (EXAFS) and x-ray absorption spectroscopy (XAS) edge studies of the CO-free, electron paramagnetic resonance-silent form of CODH from Clostridium thermoaceticum indicate a NiS4 (15) or =NiS2(O/N)2 (16) coordination environment with distorted square-planar or pyramidal geometry (16). EXAFS further suggests that an Fe-S cluster may be nearby (15). The CODH from Rhodospirillum rubrum (Rr-CODH) is a simpler enzyme (62-kDa monomer, 1 Ni and 8 Fe/S) that only oxidizes CO (8, 9). Isotopically induced electron paramagnetic resonance line-broadening suggests that Ni is covalently coupled to one or both Fe4S4 clusters in Rr-CODH and in other enzymes as well (17)(18)(19)(20). The possibility of an NiFe3S4 cubane-type cluster has been recognized (20), and alternative models exist in which Ni is bridged to Fe-S centers. Elucidation of the Ni-site structure is essential to understanding its role in catalysis. Toward that end, we report Ni K-edge XAS results for Rr-CODH. MATERIALS AND METHODSSample Preparations. Rr-CODH was purified and assayed as described (21). Purified Rr-CODH had a specific activity of 5200 gmol of CO oxidized per min-mg and contained 1.2 Ni and 8.1 Fe per mol of enzyme as determined by plasma emission spectroscopy. Rr-CODH samples were prepared for spectroscopic studies in an anaerobic glove box [Vacuum Atmospheres (Hawthorne, CA) Dri-Lab glove box model HE-493] containing an N2 atmosphere with <1 ppm 02. Rr-CODH samples in 100 mM Mops buffer, pH 7.5, were oxidized with indigo carmine as described (22) and were concentrated to 1.25 mM in a collodion ultrafiltration apparatus (Schleicher & Schuell). Some of the concentrated protein sample was reduced by adding sodium dithionite (5 mM final concentration dithionite). The oxidized and reduced samples were loaded into "140 IL XAS lucite cells (23 x 2 x 3 mm) wi...

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Tetrahedral mercaptide complexes. Crystal and molecular structures of [(C6H5)4P]2M(SC6H5)4 complexes (M = cadmium(II), zinc(II), nickel(II), cobalt(II), and manganese(II))

Cited by 206 publications

References 3 publications

Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.

Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.

Site‐Specific Substituted Cobalt(II) Horse Liver Alcohol Dehydrogenases

On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

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