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PubMed1997

Primary sequence and refined tertiary structure of Pseudomonas fluorescens holo azurin at 2.05 A.

This paper reports the primary sequence and refined crystal structure of Pseudomonas fluorescens holoazurin. The crystal structure has been determined by molecular replacement on the basis of the molecular model of azurin from Alcaligenes denitrificans, and refined by the method of molecular dynamics simulation and energy-restrained least-squares methods. P. fluorescens was crystallized in the orthorhombic space group P2(1)2(1)2(1) with unit-cell dimensions a = 31.95, b = 43.78, c = 78.81 A. The asymmetric unit is composed of only one molecule. The final R value is 16.7% for 6691 reflections to a resolution of 2.05 A. This azurin structure shows some interesting features at His35 and His83. Part of the main chain of strand 3 including His35 O are involved in the contact between two symmetrically related molecules. P. fluorescens is also compared with the other azurin structures in terms of primary sequence, crystal packing, solvent structure and Cu-site geometry. The difference in fluorescence decay behavior of two holoazurins from P. fluorescens and P. aeruginosa and the correlation between the fluorescence quenching and electron transfer are discussed.

Journal Article↗
PubMed1996

Structure Solution of Azurin II from Alcaligenes xylosoxidans using the Laue Method: Possibility of Studying In Situ Redox Changes using X-rays.

We have recently demonstrated that X-rays can be used for changing the redox states of the metal centre in metalloproteins [Murphy et al. (1995). J. Synchrotron Rad. 2, 64-69]. The possibility of using the Laue method for studying the structural changes associated with such X-ray-induced reactions is explored by applying the method to the structure determination of a new azurin (hereafter referred to as azurin II) from the denitrifying bacterium Alcaligenes xylosoxidans. Laue X-ray diffraction data of azurin II were collected at station 9.7 of the SRS Daresbury. Three diffraction patterns were recorded on film packs at three different crystal orientations. The data were processed using the Daresbury Laue Software Suite to give 2224 independent single reflections (R(merge) = 0.136) in the wavelength range 0.36-1.40 A. The data completeness was 44% at 2.55 A resolution. Phase determination for the data was undertaken using the molecular-replacement method; the top peak was chosen in both the rotation function and the subsequent translation function. This solution agreed well with the molecular-replacement solution achieved independently using monochromatic data. The electron-density map showed reasonably good agreement with the model and the copper site was readily recognizable as it had the highest density. To see if the electron-density map could be improved, ;the doublets in the diffraction data were then deconvoluted. This added 26% data in the region infinity-2d(min) resulting in an improvement in the data completeness to 50% and thus in improved continuity of the electron-density map. The quality of these maps is discussed from the point of view of the suitability of this approach for studying redox-induced structural changes.

Journal Article↗
PubMed1999

The binding of imidazole in an azurin-like blue-copper site.

Frozen solutions of the azurin mutant His117Gly in the presence of excess of methyl-substituted imidazoles have been investigated by electron spin-echo envelope modulation (ESEEM) spectroscopy at 9 GHz. The addition of imidazole is known to reconstitute a blue-copper site and variation of the non-protein bound ligand [N-methyl-, 2-methyl-, 4(5)-methylimidazole] has allowed the study of the copper-imidazole binding as a model for histidine binding in such sites. Quadrupole and hyperfine tensors of the remote nitrogen of the imidazoles have been determined. The quadrupole tensors indicate that the methyl-substituted imidazoles in the mutant adopt the same orientation relative to copper as the histidine-117 in the wild-type protein. Analysis of the hyperfine tensors in terms of spin densities reveals that the spin density on the remote nitrogen of the substituted imidazole has sigma and a variable pi character, depending on the position of the methyl group. For azurin the corresponding spin density is of virtually pure sigma character. In conclusion, blue-copper sites show subtle variations as regards the histidine/imidazole centred part of the wavefunction of the unpaired electron.

Azurin↗
PubMed2003

Active site modeling in copper azurin molecular dynamics simulations.

Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the polypeptide chain, using for the ligand residues a set of charges that is modified with respect to the apo form of the protein by the presence of the copper ion. The results show that the different charge values do not lead to relevant effects on the geometry of the active site of the protein, as long as bond distance constraints are used for all the five ligand atoms. The distance constraint on the O atom of Gly45 can be removed without altering the active site geometry. The coordination between Cu and the other axial ligand Met121 is outlined as being flexible. Differences are found between the bonds of the copper ion with the two apparently equivalent N(delta1) atoms of His46 and His117. The overall findings are discussed in connection with the issue of determining a model for the active site of azurin suitable to be used in molecular dynamics simulations under unfolding conditions.

Azurin↗
PubMed1989

Expression of the blue copper protein azurin from Pseudomonas aeruginosa in Escherichia coli.

The structural gene for the blue copper protein azurin from Pseudomonas aeruginosa has been subcloned in different expression plasmid vectors. The highest yield of expression was obtained when the gene with its native ribosome-binding site was placed downstream of the lac promoter in plasmid pUC18. The protein is exported to the periplasmic space in Escherichia coli and the amount corresponds to 27% of the total protein content in the periplasmic space. The preprotein is cleaved correctly according to N-terminal sequencing of the purified protein. Azurin has been purified in large amounts and is spectroscopically indistinguishable from the protein purified from P. aeruginosa.

Azurin↗
PubMed1987

The tertiary structure of azurin from Pseudomonas denitrificans as determined by Cu resonant diffraction using synchrotron radiation.

The structure of Pseudomonas denitrificans azurin has been solved at 3.0 A resolution by film data collection methods using synchrotron radiation. Bijvoet pairs of reflections were collected using 8.98 keV radiation where both delta f' and delta f", the real and imaginary corrections to azurin's Cu prosthetic group scattering, respectively, are large, and using 8.00 keV radiation where these corrections are smaller. The Cu atom was located by difference Patterson syntheses and used to phase the observed protein structure-factor moduli of selected reflections. An atomic model of the protein was built using a restricted data set and phases for all observed reflections to 3.0 A resolution were subsequently calculated from the initial model. The atomic model was subsequently rebuilt using all observed data. The results of this work are presented here and illustrate the utility of synchrotron radiation phasing techniques in solving the structures of metalloproteins without recourse to multiple isomorphous replacement.

Azurin↗
PubMed1995

Disruption of the disulfide bridge in azurin from Pseudomonas aeruginosa.

In the family of small blue-copper proteins azurins are unique in that they contain a disulfide bridge close to the amino-terminal end. It is situated in the 'south' side of the molecule, about 25 A away from the copper. Site-specific mutagenesis was used to exchange one or both of the cysteines in the bridge for serines in Pseudomonas aeruginosa azurin. In the double mutant Cys3Ser-Cys26Ser the Type 1 Cu is converted into Type 2, and the fluorescence of the single internal tryptophan shows that it becomes exposed to a polar environment. The circular dichroism spectrum indicates a loss of beta-structure. Thus, this mutation prevents the correct folding of the protein and the formation of the metal-binding site. Single mutants, Cys3Ser or Cys26Ser, can at least in part form native-like structures as shown by optical, EPR, fluorescence and CD spectroscopy. The Cys3Ser mutant can form a stable intermolecular disulfide bond which promotes the native conformation of the protein.

Azurin↗
PubMed1995

Electron tunneling in azurin: the coupling across a beta-sheet.

BACKGROUND: We would like to understand how electron flow is controlled in biological molecules. Standard theories calculate the rate for long distance electron transfer (ET) as the product of electronic coupling (the square of the electron tunneling matrix element) and nuclear (Franck-Condon) factors. Much attention has been directed to the role of protein secondary and tertiary structure in the tunneling coupling, focusing on the interplay between different types of chemical bonds. Here we have evaluated the relative contributions of covalent bonds, hydrogen bonds and through-space jumps in coupling through a beta-strand or across a beta-sheet section of a blue copper protein, azurin. RESULTS: We have analyzed four distant electronic couplings in azurin. Each coupling is between the copper atom and a Ru(bpy)2(im) complex attached to a histidine on the protein surface. In three experiments the intervening medium was a simple beta-strand, while in the fourth experiment it was a section of beta-sheet. CONCLUSIONS: We have shown that electron tunneling in a protein can be broken down into ET 'tubes' of pathways through specific covalent and hydrogen bonds. These ET tubes encapsulate trivial interference effects and can expose crucial inter-tube interference effects. In coupling through a beta-sheet, hydrogen bonds are as important as covalent links, and are the primary source for tube interference.

Azurin↗
PubMed2003

The significance of the flexible loop in the azurin (Az-iso2) from the obligate methylotroph Methylomonas sp. strain J.

The obligate methylotroph Methylomonas sp. strain J produces two azurins (Az-iso1 and Az-iso2) as candidates for electron acceptor from methylamine dehydrogenase (MADH) in the electron-transfer process involving the oxidation of methylamine to formaldehyde and ammonia. The X-ray crystallographic study indicated that Az-iso2 gives two types of crystals (form I and form II) with polyethylene glycol (PEG4000) and ammonium sulfate as the precipitants, respectively. Comparison between the two Az-iso2 structures in forms I and II reveals the remarkable structural changes at the top surface of the molecule around the copper atom. Az-iso2 possesses Gly43 instead of Val43 or Ala43, which is unique among all other azurins around the copper ligand His46, inducing the remarkable structural change in the loop region from Gly37 to Gly43. When the structure of Az-iso2 is superimposed on that of amicyanin in the ternary complex composed of MADH, amicyanin, and cytochrome c(551), the loop of Az-iso2 deeply overlaps with the light subunit of MADH. However, the Az-iso2 molecule is probably able to avoid any steric hindrance with the cognate MADH to form the complex for intermolecular electron-transfer reaction, since the loop containing Gly43 is flexible. We discuss why the electron-transfer activity of Az-iso2 is fivefold higher than that of Az-iso1.

Azurin↗
PubMed1993

Low frequency EPR of Pseudomonas aeruginosa azurin. Analysis of ligand superhyperfine structure from a type 1 copper site.

The type 1 copper in Pseudomonas aeruginosa azurin was studied by electron paramagnetic resonance (EPR) spectroscopy at low microwave frequencies. Partially resolved ligand hyperfine structure was observed in the perpendicular region of the spectra at both S-band (2.4 GHz) and L-band (1.1 GHz). A trial and error method, requiring several hundred simulations, has been used to simulate the low frequency EPR data and yield an optimum value of 30 MHz for ACUx, more than one half that previously reported. The fit between the simulated and experimental data is sensitive to changes in the Euler angles and, in particular, to the angle alpha which rotates the Cu A-tensor about the z-axis. Thus, the A- and g-tensors for copper in P. aeruginosa azurin do not appear to be coincident. A value for the Euler angle beta of at least 10 degrees does not disturb the fit between the simulated and experimental data. These studies demonstrate the advantage of evaluating EPR parameters from simulations at more than one frequency, especially at low frequencies where ligand superhyperfine structure may be resolved for type 1 copper.

Azurin↗
PubMed1998

Metal coordination of azurin in the unfolded state.

1H NMR data applied to the paramagnetic cobalt(II) derivative of azurin from Pseudomonas aeruginosa have made it possible to show that the metal ion is bound to the protein in the unfolded state. The relaxation data as well as the low magnetic anisotropy of the metal ion indicate that the cobalt ion is tetrahedral in the unfolded form. The cobalt ligands have been identified as the residues Gly45, His46, Cys112 and His117. Met121 is not coordinated in the unfolded state. In this state, the metal ion is not constrained to adopt a bipyramidal geometry, as imposed by the protein when it is folded. This is clear confirmation of the rack-induced bonding mechanism previously proposed for the metal ion in azurin.

Azurin↗
PubMed1993

Intramolecular electron transfer in single-site-mutated azurins.

Single-site mutants of the blue, single-copper protein, azurin, from Pseudomonas aeruginosa were reduced by CO2- radicals in pulse radiolysis experiments. The single disulfide group was reduced directly by CO2- with rates similar to those of the native protein [Farver, O., & Pecht, I. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 6968-6972]. The RSSR- radical produced in the above reaction was reoxidized in a slower intramolecular electron-transfer process (30-70 s-1 at 298 K) concomitant with a further reduction of the Cu(II) ion. The temperature dependence of the latter rates was determined and used to derive information on the possible effects of the mutations. The substitution of residue Phe114, situated on the opposite side of Cu relative to the disulfide, by Ala resulted in a rate increase by a factor of almost 2. By assuming that this effect is only due to an increase in driving force, lambda = 135 kJ mol-1 for the reorganization energy was derived. When Trp48, situated midway between the donor and the acceptor, was replaced by Leu or Met, only a small change in the rate of intramolecular electron transfer was observed, indicating that the aromatic residue in this position is apparently only marginally involved in electron transfer in wild-type azurin. Pathway calculations also suggest that a longer, through-backbone path is more efficient than the shorter one involving Trp48. The former pathway yields an exponential decay factor, beta, of 6.6 nm-1. Another mutation, raising the electron-transfer driving force, was produced by changing the Cu ligand Met121 to Leu, which increases the reduction potential by 100 mV.(ABSTRACT TRUNCATED AT 250 WORDS)

Azurin↗
PubMed1993

Resonance Raman spectroscopy of the azurin His117Gly mutant. Interconversion of type 1 and type 2 copper sites through exogenous ligands.

The copper center of the Pseudomonas aeruginosa His117Gly azurin mutant is accessible to exogenous ligands through an aperture in its surface created by the removal of the endogenous imidazole ligand. Depending on the exogenous ligand, a surprising variety of type 1 and type 2 copper sites can be obtained that are readily distinguished by electronic, EPR, and resonance Raman (RR) spectroscopy. The RR spectrum of type 1 H117G with exogenous imidazole is nearly identical to that of wild-type azurin, indicating that the trigonal geometry and short Cu-S(Cys) bond of approximately 2.15 A have been maintained. With anionic ligands (e.g., Cl-, Br-, N3-), the RR spectra show increased intensity at 370 and 400 cm-1 and a corresponding decrease in intensity at 410 cm-1, suggesting a lengthening of the Cu-S(Cys) bond as the site achieves a more tetrahedral character. An extreme example is the hydroxide adduct of H117G which is green in color and has optical and RR spectra reminiscent of the tetrahedral type 1 site in Achromobacter cycloclastes nitrite reductase. The fact that the basic RR pattern is little changed in most of the type 1 adducts indicates that the RR spectrum is due primarily to vibrations of the Cu-cysteinate moiety and that its coplanar conformation is conserved. Type 2 H117G proteins are formed by the addition of bidentate exogenous ligands such as histidine and histamine. They have their absorption maxima blue-shifted to 400 nm and their EPR A parallel values increased to approximately 160 x 10(-4) cm-1, both of which are characteristic of tetragonal Cu sites with Cu-S(thiolate) bonds of > 2.25 A. The RR spectra of the type 2 H117G proteins are still dominated by multiple cysteinate-related vibrational modes. However, the vibrational modes with the greatest intensity and Cu-S(Cys) stretching character have shifted approximately 100 cm-1 to lower energy compared to the type 1 sites, consistent with a longer (Cys)S-Cu bond. It is proposed that the tetragonal type 2 character of the bidentate ligand complexes is due to the addition of a fourth strong ligand in the equatorial ligand plane.

Anions↗
PubMed1989

A time-resolved fluorescence study of azurin and metalloazurin derivatives.

Nickel and cobalt derivatives of Pseudomonas fluorescens (ATCC 13525) azurin were prepared and their steady-state fluorescence and time-resolved fluorescence monitored. Like the copper-containing native protein, the fluorescence decay of both metallo derivatives was best fit to a sum of three exponentials, whereas the apoazurin from which they were prepared obeyed single-exponential decay kinetics. However, comparison of the lifetimes and fractional of each of the components in these derivatives to those in the oxidized and reduced native proteins revealed significant differences. These results suggest that the presence of a metal center in azurin imparts a conformational heterogeneity which is strongly dependent on the nature of the metal center. Further, the results are used to comment on current ideas concerning the geometry of the active site in this redox protein.

Azurin↗
PubMed1977

Tyrosine emission in the tryptophanless azurin from Pseudomonas fluorescens.

A strain of Pseudomonas fluorescens contains an azurin with no tryptophan and two tyrosines. This protein is interesting because it allows one to study both the structure of azurin and the emission of tyrosines in proteins. Comprehensive measurements were carried out including spectrophotometric and fluorimetric titration, fluorescence quantum yield, fluorescence polarization, and I- quenching. In the copper-containing protein, almost independent of the copper ion oxidation, the fluorescence quantum yield is approximately 60% of that of the apoprotein. The latter has the remarkable property that its quantum yield is even greater than free tyrosine. The two tyrosines in the metalloprotein have different pKa's, 10.75 and 12.78, but there is only one average pKa, 10.9 in the apoprotein. The polarization of the fluorescence at 310 nm (290-nm excitation) is 0.32 for the metalloproteins and 0.34 for the apoprotein. I- hardly quenches the fluorescence. The conclusion is that the two tyrosines are inaccesible to the solvent, located in nonpolar environments, larger than or equal to 20 A apart, and not adjacent to the disulfide bridge.

Azurin↗
PubMed1996

Dimerization of a His117Gly azurin mutant by external addition of 1,omega-di(imidazol-1-yl)alkanes.

The possibility to construct non-covalently linked protein dimers was investigated by employing the His117Gly mutant of the Cu containing azurin and the bifunctional 1,omega-di(imidazol-1-yl)alkanes as linkers. The His117Gly mutation creates a gap in the coordination sphere of the metal through which the latter becomes accessible for externally added ligands. The bifunctional ligands gave rise to the formation of dimers provided the linker was sufficiently long, as in the case of 1,omega-di(imidazol-1-yl)pentane and -hexane; the butane linker only produced monomers. The binding of the azurin molecules to the bifunctional C5 and C6 linkers showed cooperativity, which is the result of the hydrophobic interaction of the aligned hydrophobic patches. The energy and surface area involved in this process have been estimated from the experimental data to be delta G is -1.3 to -2.1 kcal/mol and 65-105 A2. The implications for the study of electron transfer processes inside a protein matrix are indicated.

Alkanes↗
PubMed1999

Backbone dynamics of azurin in solution: slow conformational change associated with deprotonation of histidine 35.

15N relaxation measurements have been performed on the type Iota blue copper protein azurin from Pseudomonas aeruginosa. The relaxation times show that one loop (residues 103-108) and one turn (residues 74-77) display fast internal motions. The rest of the protein is rigid with an average order parameter S(2) of 0.85 +/- 0. 05. The copper binding site shows the same degree of rigidity even though is it composed of several loops and lies outside the beta-sheet sandwich. Substantial exchange broadening was found for a number of residues surrounding the side chain of His-35. The average exchange rate has been determined from NMR exchange spectroscopy experiments and is 45 +/- 6 s(-)(1) at 41 degrees C. The exchange broadening is caused by the protonation/deprotonation equilibrium of His-35. The NMR results indicate that the two structures of azurin observed by X-ray diffraction of crystals at pH 5.5 and 9.0 [Nar, H., Messerschmidt, A., Huber, R., Van de Kamp, M., Canters, G. W. (1991) J. Mol. Biol. 221, 765-772] are present in solution and that they interconvert slowly.

Azurin↗
PubMed2006

Spectroscopic characterizations of bridging cysteine ligand variants of an engineered Cu2(Scys)2 CuA azurin.

Bridging cysteine ligands of the Cu(A) center in an engineered Cu(A) azurin were replaced with serine, and the variants (Cys116Ser and Cys112Ser Cu(A) azurin) were characterized by mass spectrometry, as well as UV-vis and electron paramagnetic resonance (EPR) spectroscopic techniques. The replacements resulted in dramatically perturbed spectroscopic properties, indicating that the cysteines play a critical role in maintaining the structural integrity of the Cu center. The replacements at different cysteine residues resulted in different perturbations, even though the two cysteines are geometrically symmetrical in the primary coordination sphere with respect to the two copper ions. The Cys112Ser variant contains two distinct type 2 copper centers, while the Cys116Ser variant has one type 1 copper center with slight tetragonal distortion. Both the UV-vis and EPR spectra of the Cys116Ser variant change with pH, and the pK(a) of the transition is 6.0. A type 1 copper EPR spectrum with A(||) = 26 G was obtained at pH 7.0, while a type 2 copper EPR spectrum with A(||) = 140 G was found at pH 5.0. Interestingly, lowering the temperature from 290 to 85 K resulted in conversion of the Cys116Ser variant from a type 1 copper center to a type 2 copper center, suggesting rearrangement of the ligand around the copper or binding of an exogenous ligand at low temperature. This difference in mutation effects at different cysteines may be due to different constraints exerted on the two cysteines by hydrogen-bonding patterns in the ligand loop.

Azurin↗