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At least 649 records · Page 36Linked to original sources
PubMed1986

Sulfate-dependent iron oxidation by Thiobacillus ferrooxidans: characterization of a new EPR detectable electron transport component on the reducing side of rusticyanin.

Iron(II) oxidation by pH 2.5 HCl-washed cells of Thiobacillus ferrooxidans is known to be sulfate dependent. Sulfate dependence of the autooxidation of a novel component in the electron transport pathway is demonstrated. This component exhibits an electron paramagnetic resonance (EPR) signal in the oxidized state at g = 2.005 distinguishable from the g = 2.08 signal attributed to rusticyanin. The novel component is proposed to be a three-iron-sulfur cluster based upon the g value, lineshape, and temperature dependence. Oxyanion specificity for the EPR signal has the same dependence on sulfate as does iron(II) oxidation. By using azide to inhibit electron transfer to oxygen, sulfate was shown to be involved in electron transfer from the g = 2.005 component to the copper of rusticyanin.

Anions↗
PubMed1981

Electron paramagnetic resonance studies of Pseudomonas cytochrome c peroxidase.

The EPR spectrum at 15 K of Pseudomonas cytochrome c peroxidase, which contains two hemes per molecule, is in the totally ferric form characteristic of low-spin heme giving two sets of g-values with gz 3.26 and 2.94. These values indicate an imidazole-nitrogen : heme-iron : methionine-sulfur and an imidazole-nitrogen : heme-iron : imidazole-nitrogen hemochrome structure, respectively. The spectrum is essentially identical at pH 6.0 and 4.6 and shows only a very small amount of high-spin heme iron (g 5--6) also at 77 K. Interaction between the two hemes is shown to exist by experiments in which one heme is reduced. This induces a change of the EPR signal of the other (to gz 2.83, gy 2.35 and gx 1.54), indicative of the removal of a histidine proton from that heme, which is axially coordinated to two histidine residues. If hydrogen peroxide is added to the partially reduced protein, its EPR signal is replaced by still other signals (gz 3.5 and 3.15). Only a very small free radical peak could be observed consistent with earlier mechanistic proposals. Contrary to the EPR spectra recorded at low temperature, the optical absorption spectra of both totally oxidized and partially reduced enzyme reveal the presence of high-spin heme at room temperature. It seems that a transition of one of the heme c moieties from an essentially high-spin to a low-spin form takes place on cooling the enzyme from 298 to 15 K.

Azurin↗
PubMed1989

Cytochrome oxidase of an acidophilic iron-oxidizing bacterium, Thiobacillus ferrooxidans, functions at pH 3.5.

Cytochrome oxidase of Thiobacillus ferrooxidans was partially purified. The oxidase preparation had haems a and c, and oxidized ferrocytochrome c-552 of the bacterium. The optimal pH of the reaction was 3.5. The enzyme also oxidized the reduced form of rusticyanin, a copper protein of the bacterium. Our results indicate that the reduction of molecular oxygen by this enzyme may occur in the periplasm.

Azurin↗
PubMed1990

EXAFS of the type-1 copper site of rusticyanin.

Extended X-ray absorption fine structure (EXAFS) spectra at the Cu K-edge have been recorded of the oxidized and reduced form at pH 3.5 of rusticyanin, the type-1 or 'blue'-copper protein from Thiobacillus ferrooxidans. The EXAFS of oxidized rusticyanin is well simulated with models assuming a ligand set of 2 N(His) and 1 S(Cys) at 1.99 and 2.16 A, respectively. Upon reduction, the average Cu-N ligand distance increases by approx. 0.08A. For both redox states studied, the fit by the simulation is significantly improved by including a contribution of an additional sulfur ligand at approx. 2.8 A. From comparison with structural data of other blue-copper proteins, it is concluded that the copper coordination environment is relatively rigid, which may be a clue to its high redox potential.

Azurin↗
PubMed1991

A structure-derived sequence pattern for the detection of type I copper binding domains in distantly related proteins.

A structure-based approach to the definition of sequence patterns characteristic of protein domains is presented by example. The approach requires a multiple sequence alignment of a family (or set of related families) as well as at least one three-dimensional structure. The pattern derived does not merely summarize the information in the known sequences but attempts to generalize the pattern specifications based on structural insight. In this example, the pattern-driven database search identified correctly most of the known type I copper-binding domains and detected the presence of a homologous domain in a previously unknown case (CopA protein). The significance of these results is discussed.

Amino Acid Sequence↗
PubMed1992

The amino acid sequence of a type I copper protein with an unusual serine- and hydroxyproline-rich C-terminal domain isolated from cucumber peelings.

We have determined the amino acid sequence of a small copper protein isolated from cucumber peelings. This cupredoxin contains 137 amino acids including a pyroglutamate as the first residue. The N-terminal 110 amino acid-long domain shows 30-37% identity to 2 other cupredoxins, stellacyanin and cucumber basic blue protein. A unique feature of this protein is a 27 amino acid-long C-terminal domain rich in 4-hydroxyproline and serine and resembling certain plant cell wall proteins. The prolines in this domain are hydroxylated to a different extent depending on the surrounding sequence.

Amino Acid Sequence↗
PubMed1993

Engineering type 1 copper sites in proteins.

The use of site-directed mutagenesis methods has revolutionalized the study of the so-called type 1 and type 2 copper sites in proteins. In particular our understanding of the relation between the structure, and the mechanistic and spectroscopic features of these sites is benefitting from the application of these techniques. Recent progress in the field is reviewed with emphasis on the study of type 1 sites. Topics covered comprise the characteristics of the natural type 1 and type 2 sites, the genetics of blue copper proteins, the modification of Cu sites, the spectroscopy of natural and engineered type 1 and type 2 sites, the effect of mutations on midpoint potentials and the mechanism of electron transfer as carried out by the blue copper proteins.

Azurin↗
PubMed1994

The crystal structures of reduced pseudoazurin from Alcaligenes faecalis S-6 at two pH values.

The structures of the reduced (Cu1+) blue-copper protein pseudoazurin from Alcaligenes faecalis strain S-6 are refined at pH 7.8 and 4.4 using X-ray diffraction data to 1.8 A resolution. The final R-factors for the high and low pH structures are 0.178 and 0.177, respectively. Comparing the reduced pseudoazurin at pH 7.8 with the oxidised (Cu2+) molecule, small changes are observed in the vicinity of the copper site and on the protein surface. At pH 4.4 the copper substituent imidazole of His81 rotates away from the metal with a concurrent movement of the latter towards the plane of the remaining three ligands (S gamma-Cys78, N delta 1-His40 and S delta-Met86) thus the geometry of the copper site becomes planar trigonal.

Alcaligenes↗
PubMed1995

Complete 13C assignments for recombinant Cu(I) rusticyanin. Prediction of secondary structure from patterns of chemical shifts.

Complete resonance assignments for the 13C spectrum of reduced (Cu(I)) rusticyanin have been made using 13C, 15N doubly labeled recombinant material. The reported assignments include those for the carboxyl and carbonyl carbon atoms and protonated aromatic ring carbons, and were obtained using a variety of 2- and 3D inverse-detected NMR experiments, including 13C, 15N, 1H triple resonance experiments and HCCH-COSY and -TOCSY. Backbone carbonyl assignments were obtained using 3D HNCO and HCACO spectra, and modified versions of 2D H(CA)CO and HMBC spectra were used to obtain side-chain carboxyl carbon and methionine epsilon-methyl carbon assignments, respectively. A comparison of the 13C alpha, 13C beta and 13CO chemical shifts with published 'random coil' values confirms the conclusion reached from a consideration of the 3JHN alpha coupling constants and the pattern of sequential NOEs, that the protein consists largely of beta-structure.

Amino Acid Sequence↗
PubMed1995

The crystal structure of apo-pseudoazurin from Alcaligenes faecalis S-6.

The 3D structure of the apo-pseudoazurin (copper free pseudoazurin) from Alcaligenes faecalis strain S-6 is determined and refined at pH 6.7 using X-ray diffraction data to 1.85 A resolution. The final crystallographic R-factor is 0.164. Comparing the structures of apo-pseudoazurin and the native (Cu2+) protein, we observed limited differences ranging between 0.1-0.4 A at the vicinity of the copper site, at the loops connecting the secondary structural elements, at certain beta-strands and at the amino and carboxy termini of the protein.

Alcaligenes↗
PubMed1984

Twisted hyperboloid (Strophoid) as a model of beta-barrels in proteins.

Using a least-squares fitting procedure, polypeptide backbones of one parallel and seven antiparallel beta-barrels were approximated with various curved surfaces. Although the hyperboloid gave better approximations to all the beta-barrel backbones than the ellipsoid, elliptical cylinder or catenoid, the best approximations were obtained with a novel surface, a twisted hyperboloid (strophoid). The root-mean-square errors between individual beta-barrels and the fitted strophoid surfaces ranged from 0.75 A to 1.64 A. The parameters which determine the strophoid surface allow groups of beta-barrel shapes to be defined according to their barrel twists (i.e. angles subtended by directions of the long axis of cross-section at the top and the bottom of the barrel), course of elliptical cross-sections (either monotonically increasing along the barrel axis, as in cones, or having a middle "waist", as in hyperboloids), and types of backbone curvatures (either convex or concave). The curvatures at individual points of strophoid surface are local, variable quantities related to the local helicity (coil) of the polypeptide backbone, in contrast to values of beta-sheet twist (i.e. dihedral angles subtended by adjacent beta-strands) known to be virtually identical in all the beta-sheets. The variability found in parameters such as barrel shapes and curvatures suggests that simple models (isotropically stressed surfaces, principle of minimal surface tension) proposed in the past to account for beta-barrel shapes are not sufficient. Rather, the complex nature of best-fit theoretical surfaces points to an important role played by a local variability of the forces involved.

Azurin↗
PubMed1987

A sensitive procedure to compare amino acid sequences.

Methods are discussed that provide sensitive criteria for detection of weak sequence homologies. They are based on the Dayhoff relatedness odds amino acid exchange matrix and certain residue physical characteristics. The search procedure uses several residue probe lengths in comparing all possible segments of two protein sequences, and search plots are shown with peak values displayed over the entire search length. Alignments are automatically effected using the highest search matrix values and without the necessity of gap penalties. Tests for significance are derived from actual protein sequences rather than a random shuffling procedure.

Alcohol Dehydrogenase↗