Genetic switching by the Lac repressor is based on two-state Monod-Wyman-Changeux allostery

High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In the absence of ligands, the dimer exists in a dynamic equilibrium between DNA-bound and inducer-bound conformations. Binding of either effector shifts this equilibrium toward either bound state. Analysis of the ternary complex between repressor, operator DNA, and inducer shows how adding the inducer results in allosteric changes that disrupt the interdomain contacts between the inducer binding and DNA binding domains and how this in turn leads to destabilization of the hinge helices and release of the Lac repressor from the operator. Based on our data, the allosteric mechanism of the induction process is in full agreement with the well-known Monod-Wyman-Changeux model.

Sliding and target location of DNA-binding proteins: an NMR view of the lac repressor system

In non-specific lac headpiece-DNA complexes selective NMR line broadening is observed that strongly depends on length and composition of the DNA fragments. This broadening involves amide protons found in the non-specific lac-DNA structure to be interacting with the DNA phosphate backbone, and can be ascribed to DNA sliding of the protein along the DNA. This NMR exchange broadening has been used to estimate the 1D diffusion constant for sliding along non-specific DNA. The observed 1D diffusion constant of 4×10(-12) cm(2)/s is two orders of magnitude smaller than derived from previous kinetic experiments, but falls in the range of values determined more recently using single molecule methods. This strongly supports the notion that sliding could play at most a minor role in the association kinetics of binding of lac repressor to lac operator and that other processes such as hopping and intersegment transfer contribute to facilitate the DNA recognition process.

The CoxD protein of Oligotropha carboxidovorans is a predicted AAA+ ATPase chaperone involved in the biogenesis of the CO dehydrogenase [CuSMoO2] cluster

CO dehydrogenase from the Gram-negative chemolithoautotrophic eubacterium Oligotropha carboxidovorans OM5 is a structurally characterized molybdenum-containing iron-sulfur flavoenzyme, which catalyzes the oxidation of CO (CO + H(2)O --> CO(2) + 2e(-) + 2H(+)). It accommodates in its active site a unique bimetallic [CuSMoO(2)] cluster, which is subject to post-translational maturation. Insertional mutagenesis of coxD has established its requirement for the assembly of the [CuSMoO(2)] cluster. Disruption of coxD led to a phenotype of the corresponding mutant OM5 D::km with the following characteristics: (i) It was impaired in the utilization of CO, whereas the utilization of H(2) plus CO(2) was not affected; (ii) Under appropriate induction conditions bacteria synthesized a fully assembled apo-CO dehydrogenase, which could not oxidize CO; (iii) Apo-CO dehydrogenase contained a [MoO(3)] site in place of the [CuSMoO(2)] cluster; and (iv) Employing sodium sulfide first and then the Cu(I)-(thiourea)(3) complex, the non-catalytic [MoO(3)] site could be reconstituted in vitro to a [CuSMoO(2)] cluster capable of oxidizing CO. Sequence information suggests that CoxD is a MoxR-like AAA+ ATPase chaperone related to the hexameric, ring-shaped BchI component of Mg(2+)-chelatases. Recombinant CoxD, which appeared in Escherichia coli in inclusion bodies, occurs exclusively in cytoplasmic membranes of O. carboxidovorans grown in the presence of CO, and its occurrence coincided with GTPase activity upon sucrose density gradient centrifugation of cell extracts. The presumed function of CoxD is the partial unfolding of apo-CO dehydrogenase to assist in the stepwise introduction of sulfur and copper in the [MoO(3)] center of the enzyme.

Sulfur X-ray absorption spectroscopy of living mammalian cells: an enabling tool for sulfur metabolomics. In situ observation of uptake of taurine into MDCK cells

Sulfur is essential for life, with important roles in biological structure and function. However, because of a lack of suitable biophysical techniques, in situ information about sulfur biochemistry is generally difficult to obtain. Here, we present an in situ sulfur X-ray absorption spectroscopy (S-XAS) study of living cell cultures of the mammalian renal epithelial MDCK cell line. A great deal of information is retrieved from a characteristic sulfonate feature in the X-ray absorption spectrum of the cell cultures, which can be related to the amino acid taurine. We followed the time and dose dependence of uptake of taurine into MDCK cell monolayers. The corresponding uptake curves showed a typical saturation behavior with considerable levels of taurine accumulation inside the cells (as much as 40% of total cellular sulfur). We also investigated the polarity of uptake of taurine into MDCK cells, and our results confirmed that uptake in situ is predominantly a function of the basolateral cell surface.

A new type of metalloprotein: The Mo storage protein from azotobacter vinelandii contains a polynuclear molybdenum-oxide cluster

Azotobacter vinelandii is a diazotrophic bacterium characterized by the outstanding capability of storing Mo in a special storage protein, which guarantees Mo-dependent nitrogen fixation even under growth conditions of extreme Mo starvation. The Mo storage protein is constitutively synthesized with respect to the nitrogen source and is regulated by molybdenum at an extremely low concentration level (0-50 nM). This protein was isolated as an alpha4beta4 octamer with a total molecular mass of about 240 kg mol(-1) and its shape was determined by small-angle X-ray scattering. The genes of the alpha and beta subunits were unequivocally identified; the amino acid sequences thereby determined reveal that the Mo storage protein is not related to any other known molybdoprotein. Each protein molecule can store at least 90 Mo atoms. Extended X-ray absorption fine-structure spectroscopy identified a metal-oxygen cluster bound to the Mo storage protein. The binding of Mo (biosynthesis and incorporation of the cluster) is dependent on adenosine triphosphate (ATP); Mo release is ATP-independent but pH-regulated, occurring only above pH 7.1. This Mo storage protein is the only known noniron metal storage system in the biosphere containing a metal-oxygen cluster.

A novel binuclear [CuSMo] cluster at the active site of carbon monoxide dehydrogenase: characterization by X-ray absorption spectroscopy

The structurally characterized molybdoenzyme carbon monoxide dehydrogenase (CODH) catalyzes the oxidation of CO to CO2 in the aerobic bacterium Oligotropha carboxidovorans. The active site of the enzyme was studied by Mo- and Cu-K-edge X-ray absorption spectroscopy. This revealed a bimetallic [Cu(I)SMo(VI)(double bond O)2] cluster in oxidized CODH which was converted into a [Cu(I)SMo(IV)(double bond O)OH2] cluster upon reduction. The Cu...Mo distance is 3.70 A in the oxidized form and is increased to 4.23 A upon reduction. The bacteria contain CODH species with the complete and functional bimetallic cluster along with enzyme species deficient in Cu and/or bridging S. The latter are precursors in the posttranslational biosynthesis of the metal cluster. Cu-deficient CODH is the most prominent precursor and contains a [HSMo(double bond O)OH2] cluster. Se-K-edge X-ray absorption spectroscopy demonstrates that Se is coordinated by two C atoms at 1.94-1.95 A distance. This is interpreted as a replacement of the S in methionine residues. In contrast to a previous report [Dobbek, H., Gremer, L., Meyer, O., and Huber, R. (1999) Proc. Natl. Acad. Sci. U.S.A. 96, 8884-8889] Se was not identified in the active site of CODH.

The role of Se, Mo and Fe in the structure and function of carbon monoxide dehydrogenase

CO dehydrogenase (EC 1.2.99.2) catalyzes the oxidation of CO according to the following equation: CO + H2O-->CO2 + 2 e- + 2 H+. It is a selenium-containing molybdo-iron-sulfur-flavoenzyme, which has been crystallized and structurally characterized in its oxidized state from the aerobic CO utilizing bacteria Oligotropha carboxidovorans and Hydrogenophaga pseudoflava. Both CO dehydrogenase structures show only minor differences, and the enzymes are dimers of two heterotrimers. Each heterotrimer is composed of a molybdoprotein, a flavoprotein, and an iron-sulfur protein. CO oxidation takes place at the molybdoprotein which contains a 1:1 mononuclear complex of molybdopterin-cytosine dinucleotide and a Mo-ion, along with a catalytically essential S-selanylcysteine. The latter is appropriately positioned in the SeMo-active site by a unique VAYRCSFR active site loop. In H. pseudoflava the arginine preceeding the cysteine in the active site loop is modified to a Cgamma-hydroxy arginine residue which has no obvious function. The substituents in the first coordination sphere of the Mo-ion are the enedithiolate sulfur atoms of the molybdopterin-cytosine dinucleotide, two oxo- and a sulfido-group. Extended X-ray absorption fine structure spectroscopy (EXAFS), along with the crystal structure of CO dehydrogenase (23.2 U mg(-1)) at 1.85 A resolution, have identified a sulfur atom at 2.3 A from the Mo-ion. The sulfur reacts with cyanide yielding thiocyanate. The corresponding inactive desulfo-CO dehydrogenase shows a typical desulfo inhibited-type of Mo-electron paramagnetic resonance (EPR) spectrum. Structural changes at the SeMo-site during catalysis are suggested by the Mo to Se distance of 3.7 A and the Mo-S-Se angle of 113 degrees in the oxidized enzyme which increase to 4.1 A, and 121 degrees, respectively, in the reduced enzyme. The intramolecular electron transport chain in CO dehydrogenase involves the following prosthetic groups and minimal distances: CO-->[Mo of the molybdenum cofactor] - 14.6 A - [2Fe-2S]I - 12.4 A - [2Fe-2S]II - 8.7 A - [FAD].

High-Resolution Infrared and Millimeter-Wave Study of the v(3) = 1 State of HSiF(3) and DSiF(3)

Millimeter-wave spectra of HSiF(3) and DSiF(3) in the v(3) = 1 excited state have been measured from 100 to 490 GHz. Infrared spectra have been recorded in the nu(3) regions, nu(0) 424.0301 and 420.9320 cm(-1) in HSiF(3) and DSiF(3), respectively, with a resolution of 2.4 x 10(-3) cm(-1). Since in both species the parameters alpha(B)(3) and alpha(C)(3) have very similar values, no K structure could be resolved in the (Q)P and (Q)R clusters for low-to-medium K values. For high J the effect of the ground state D(JK) term more and more dominates and spreads the J clusters into opposite directions such that medium-to-high K components, particularly those with K = 3p, are resolved. Rotational and infrared data have been fitted together using a model up to sextic centrifugal distortion constants. No perturbations were indicated. Hot bands (nu(3) + nnu(6))-nnu(6) with n = 1, 2, and 3 have been detected and analyzed. Copyright 2000 Academic Press.

Radiofrequency, Centimeter-Wave, Millimeter-Wave, and Infrared Spectra of SiHF(3): Investigation of the Ground, v(4) = 1, and v(6) = 1 Vibrational States

The present paper deals with the analysis of the microwave, millimeter-wave, and infrared spectra of (28)SiHF(3) in its ground, v(6) = 1 and v(4) = 1 excited states. The former was observed up to 1055 GHz leading to the determination of one octic centrifugal distortion constant, L(J) = -0.0749(55) µHz. Furthermore the <k ||H ||k +/- 6> interaction term ||h(3,GS) || = 1.1032(70) mHz has been fitted from splittings of six K = 3 lines. The excited states have been regarded as isolated ones. This enabled fits according the Q-, D-, and QD-reduction schemes proposed by E. I. Lobodenko, O. N. Sulakshina, V. I. Perevalov, and Vl. G. Tyuterev, (J. Mol. Spectrosc. 126, 159-170 (1987)) and further developed by J. K. G. Watson, C. Gerke, H. Harder, and K. Sarka, (J. Mol. Spectrosc. 187, 131-141 (1997)) and Harder (J. Mol. Spectrosc. 194, 145 (1999)). A multiple fit analysis was performed confirming the assumption that the excited states are not affected by intervibrational resonances. Finally the millimeter spectrum of (29)SiHF(3) and (30)SiHF(3) in their ground state was also measured up to 460 GHz and accurate rotational and centrifugal distortion parameters were derived. Copyright 2000 Academic Press.