The structure of the azide coordinated superoxide dismutase of Propionibacterium shermanii investigated by X-ray structure analysis, extended X-ray absorption fine structure, Mössbauer and electron paramagnetic resonance spectroscopy

Schmidt, Marius; Scherk, C.; Яковлева, О. А.; Nolting, H.‐F.; Meier, Beate; Parak, F.

doi:10.1016/s0020-1693(97)06061-1

Cited by 12 publications

(16 citation statements)

References 16 publications

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“…By visualizing the corresponding protein structures, we often observed that the ligand atom closest to the aromatic ring was oriented so that the attached hydrogen atom would extend towards a bond rather than towards the center of the aromatic ring. [54,55,56,57] In other proteins, such as superoxide dismutase (SOD), [58,27,59,60,61] different ligands (water and asparagine) can interact with different aromatics (in SOD, two different tryptophans). Similar geometries for cation ± p interactions were found by quantum chemical calculations on the [Co(NH 3 ) 6 ] 3 À benzene model system.…”

Section: Resultsmentioning

confidence: 99%

“…[27] Data Screening and Computational Methods Crystal structures of proteins containing Ca, Co, Cr, Cu, Fe, Mg, Mn, Ni, and Zn as cations were obtained from the PDB. For this purpose, we screened crystal structures of metalloproteins in the Protein Data Bank (PDB) and studied in more detail the structures of a selection of metalloproteins in which we found this specific cation ± p interaction; between ligands coordinated to a metal cation and aromatic residues.…”

Section: Introductionmentioning

confidence: 99%

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Metal Ligand Aromatic Cation–π Interactions in Metalloproteins: Ligands Coordinated to Metal Interact with Aromatic Residues

2000

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Cation-pi interactions between aromatic residues and cationic amino groups in side chains and have been recognized as noncovalent bonding interactions relevant for molecular recognition and for stabilization and definition of the native structure of proteins. We propose a novel type of cation-pi interaction in metalloproteins; namely interaction between ligands coordinated to a metal cation--which gain positive charge from the metal--and aromatic groups in amino acid side chains. Investigation of crystal structures of metalloproteins in the Protein Data Bank (PDB) has revealed that there exist quite a number of metalloproteins in which aromatic rings of phenylalanine, tyrosine, and tryptophan are situated close to a metal center interacting with coordinated ligands. Among these ligands are amino acids such as asparagine, aspartate, glutamate, histidine, and threonine, but also water and substrates like ethanol. These interactions play a role in the stability and conformation of metalloproteins, and in some cases may also be directly involved in the mechanism of enzymatic reactions, which occur at the metal center. For the enzyme superoxide dismutase, we used quantum chemical computation to calculate that Trp163 has an interaction energy of 10.09 kcal mol(-1) with the ligands coordinated to iron.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Metal Ligand Aromatic Cation–π Interactions in Metalloproteins: Ligands Coordinated to Metal Interact with Aromatic Residues

2000

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“…At pH 10, as well as near the fluoride‐coordinated iron the difference electron density at the 6th coordination site was comparable in both subunits and much higher than 4 σ. Consequently, the occupancy values are similar for the fluoride ions and for the 6th coordinated molecules at pH 10 (65% and 70%, respectively, in both subunits). It should be mentioned that the Fe‐SOD of P. shermanii grown from a complex medium usually contains an appreciable (up to 30%, see [15]) amount of other metal ions like manganese, copper and zinc in the active center. The P. shermanii SOD is a cambialistic SOD [16,17].…”

Section: Resultsmentioning

confidence: 99%

“…Asp161 hardly moves at all and His27 remains relatively stable whereas His75 and His165 move relative to the iron. Angular and structural changes are equivalent to those induced by the binding of fluoride and azide (see also Table 6, the structure of the azide coordinated SOD was taken from [15]). No matter what kind of molecule binds to the free 6th site, similar structural changes occur.…”

Section: Resultsmentioning

confidence: 99%

Manipulating the coordination mumber of the ferric iron within the cambialistic superoxide dismutase of Propionibacterium shermanii by changing the pH‐value

Schmidt

1999

European Journal of Biochemistry

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The structure of the Propionibacterium freudenreichii subspecies shermanii superoxide dismutase (SOD) was determined at various pH values. As a comparison, the structure of the fluoride coordinated SOD was solved. The SOD crystallizes at pH 6.1 in the space group C222 1 with two subunits, A and B, in the asymmetric unit. An increase of the pH value changes the cell parameters slightly but not the symmetry of the crystals. The overall structure of the SOD remains a compact tetrameter and is comparable to that at pH 6.1 no matter whether the pH increases or fluoride is added. At values above pH 7.4, an additional hydroxide ion can bind to the active center. Its position is similar to the binding site of the fluoride. The coordination number changes from five to six if the pH increases or fluoride is added. The binding behavior of the hydroxide ion is different for subunit A and B. Structures at different pH-values are comparable with models derived by spectroscopic methods. The influence of temperature on the binding properties of the hydroxide ion was investigated using analysis of an X-ray structure solved at pH 8.1 and 140 K. Compared to the structure at room temperature, the structural changes are observable but remain small. The consequences of hydroxide binding to the iron are discussed.

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“…Large fourth-order parameters, namely a = 0.074 cm −1 and F = 0.043 cm −1 , have been reported for Fe superoxide dismutase-azide, 10 together with D = 0.46 cm −1 and E/D = 0.255. An 8.0 T Mössbauer spectrum of 1 together with a spectral simulation is shown in Figure 2A (see Figures S2 and S3 for additional spectra).…”

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confidence: 92%

Characterization of a High-Spin Non-Heme Fe^III–OOH Intermediate and Its Quantitative Conversion to an Fe^IV═O Complex

et al. 2011

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We have generated a high-spin FeIII–OOH complex supported by tetramethylcyclam via protonation of its conjugate base and characterized it in detail by various spectroscopic methods. This FeIII–OOH species converts quantitatively to an FeIV=O complex via O–O bond cleavage, which represents the first example of such a conversion. This conversion is promoted by two factors: the strong FeIII–OOH bond that inhibits Fe–O bond lysis and the addition of protons that facilitate O–O bond cleavage. This example provides a synthetic precedent for how O–O bond cleavage of high-spin iron(III)-peroxo intermediates of nonheme iron enzymes may be promoted.

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The structure of the azide coordinated superoxide dismutase of Propionibacterium shermanii investigated by X-ray structure analysis, extended X-ray absorption fine structure, Mössbauer and electron paramagnetic resonance spectroscopy

Cited by 12 publications

References 16 publications

Metal Ligand Aromatic Cation–π Interactions in Metalloproteins: Ligands Coordinated to Metal Interact with Aromatic Residues

Metal Ligand Aromatic Cation–π Interactions in Metalloproteins: Ligands Coordinated to Metal Interact with Aromatic Residues

Manipulating the coordination mumber of the ferric iron within the cambialistic superoxide dismutase of Propionibacterium shermanii by changing the pH‐value

Characterization of a High-Spin Non-Heme Fe^III–OOH Intermediate and Its Quantitative Conversion to an Fe^IV═O Complex

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The structure of the azide coordinated superoxide dismutase of Propionibacterium shermanii investigated by X-ray structure analysis, extended X-ray absorption fine structure, Mössbauer and electron paramagnetic resonance spectroscopy

Cited by 12 publications

References 16 publications

Metal Ligand Aromatic Cation–π Interactions in Metalloproteins: Ligands Coordinated to Metal Interact with Aromatic Residues

Metal Ligand Aromatic Cation–π Interactions in Metalloproteins: Ligands Coordinated to Metal Interact with Aromatic Residues

Manipulating the coordination mumber of the ferric iron within the cambialistic superoxide dismutase of Propionibacterium shermanii by changing the pH‐value

Characterization of a High-Spin Non-Heme FeIII–OOH Intermediate and Its Quantitative Conversion to an FeIV═O Complex

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Characterization of a High-Spin Non-Heme Fe^III–OOH Intermediate and Its Quantitative Conversion to an Fe^IV═O Complex