Crystal structure of yeast Cu,Zn superoxide dismutase

Djinović, K.; Gatti, Giuseppina; Coda, Alessandro; Antolini, Luciano; Pelosi, Giorgio; Desideri, Alessandro; Falconi, Mattia; Marmocchi, Franco; Rotilio, Giuseppe; Bolognesi, Martino

doi:10.1016/0022-2836(92)90401-5

Cited by 113 publications

(72 citation statements)

References 45 publications

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“…Residue Glu88, in subunit B, forms a salt bridge with the basic guanidinium group of a symmetry-related Argl41, the most important residue for substrate attraction and orientation in the active-site pocket. The guanidinium group of Argl41 is at 6.81 and 7.06 ,~ (in subunits A and B, respectively) from the Cu 2+ center, similar to what is observed in the BCo-SOD and Y-SOD crystal structures Djinovi6, Gatti et al, 1992). Despite the salt bridge, the side-chain conformation of Argl41 is almost identical in the two crystallographically independent X-SODb subunits, the orientation of the side chain being defined by strong hydrogen bonds between Argl41 atoms NH1 and NH2 and carbonyl O atoms of residues Cys55 and Gly59.…”

Section: Crystal Contactssupporting

confidence: 74%

“…Among these, W177 and W168 hydrogen bond to the carbonyl O atom of Gly139, as well as to the Argl41 NE atom, contributing to the Argl41 side-chain orientation. A remarkably similar solvent organization in the active-site channel has been observed in the BCo-SOD and Y-SOD structures Djinovi6, Gatti et al, 1992), which display quite comparable catalytic constants (O'Neill et al, 1988), suggesting a role of active-site solvent structure in promoting the functional properties of the enzyme.…”

Section: Solvent Structurementioning

confidence: 53%

“…These interactions, which are relevant for the active-site structural organization, are conserved in the other known SOD three-dimensional structures (Bordo et al, 1994). Moreover, hydrogen-bonding interactions involving water molecules in the active site are also substantially conserved, as compared to BCo-SOD as well as Y-SOD Djinovi6, Gatti et al, 1992), and are discussed below.…”

Section: X-sodb Active-site Structurementioning

confidence: 94%

“…Three-dimensional structures are known in detail for the (oxidized) Cu, Zn SOD from four different species, namely ox (Tainer, Getzoff, Beem, Richardson & Richardson, 1982), spinach (Kitagawa et al, 1991), yeast (Djinovi6, Gatti et al, 1992) and human (Parge, Hallewell & Tainer, 1992), together with the semisynthetic Cu,Co bovine SOD (Djinovir, Coda et al, 1992). The central structural core of the SOD subunit is a flattened Greek-key /3-barrel motif consisting of eight antiparallel /3-strands joined by three external loops (Fig.…”

Section: Introductionmentioning

confidence: 99%

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Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 Å resolution

Djinović-Carugo¹,

Battistoni²,

Carri³

et al. 1996

Acta Cryst D

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AbbreviationsXenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has been crystallized and the structure determined at 1.49A, resolution. The crystals belong to space group P2~2~2~, with cell constants a=73.33, b = 68.86, c = 59.73 A, and contain one dimeric molecule of Mr 32000 per asymmetric unit. The structure was solved by molecular-replacement techniques using the semisynthetic Cu,Co bovine enzyme as search model, and refined by molecular dynamics with a crystallographic pseudo-energy term. During the final steps, positional and anisotropic thermal parameters of the atoms were refined. The R factor for the 49 209 unique reflections in the 10.0-1.49 A, resolution range is 0.104, for a model comprising 2023 protein atoms, two Cu 2+, two Zn 2+, and 353 water molecules. The overall temperature factor for the model, including solvent, is 20.3 A, 2, while the calculated r.m.s, coordinate error for the refined model is 0.036A,. As suggested by the primary structure homology to any other known intracellular eukaryotic superoxide dismutase (> 50%), the typical structural scaffolding of flattened antiparallel eight-stranded (J-barrel is well conserved in X. laevis Cu,Zn superoxide dismutase b, together with the coordination geometry of the metal centers in the active site. The higher thermal stability of the bb X. laevis superoxide dismutase homodimer, with respect to dimers involving the a-type isoenzyme subunit(s), can be related, on the basis of the high-resolution structure, to side-chain and solvent interactions centered on residue Tyr149, in both b-type subunits. The analysis of the overall solvent structure reveals a number of equivalent water molecule sites in the two subunits, and in homologous superoxide dismutase models. Their locations are discussed in detail and classified on the basis of their structural role.

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Section: Crystal Contactssupporting

confidence: 74%

Section: Solvent Structurementioning

confidence: 53%

Section: X-sodb Active-site Structurementioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 Å resolution

Djinović-Carugo¹,

Battistoni²,

Carri³

et al. 1996

Acta Cryst D

Self Cite

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“…The active site comprises the redox active copper with square planar coordination to four histidines (Scheme 1A); one of each is a bridging ligand of copper and zinc. The other zinc ligands are two histidines and a monodentate aspartate (5,7,8). A channel across the protein leads to the copper, toward a fifth axial coordination position, occupied by a water molecule in the oxidized enzyme, which is available for inhibitors and possibly for the superoxide substrate (Scheme 1B) (14 -16).…”

mentioning

confidence: 99%

Long Distance Charge Redistribution Upon Cu,Zn-Superoxide Dismutase Reduction

Dupeyrat

Vidaud

Lorphelin

et al. 2004

Journal of Biological Chemistry

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Cu,Zn-superoxide dismutase (Cu,Zn-SOD) is a ubiquitous enzyme with an essential role in antioxidant defense. To better understand structural factors at the origin of the highly efficient superoxide dismutation mechanism, we analyzed the consequence of copper reduction on the electronic properties of the backbone and individual amino acids by using electrochemistry coupled to Fourier transform infrared spectroscopy. Comparison of data recorded with bovine erythrocyte and recombinant chloroplastic Cu,Zn-SOD from Lycopersicon esculentum, expressed as a functional tetramer in Escherichia coli and 14 N-or fully 15 N-labeled, demonstrated that the infrared changes were dominated by reorganizations of peptide bonds and histidine copper ligands. Two main infrared modes of histidine side chain, markers of metal coordination, were identified by using Cu-and Zn-methylimidazole models: the (C 4 C 5 ) at 1605-1594 cm ؊1 or Ϸ1586 cm ؊1 for N or N coordination, and the (C 5 N ) at Ϸ1113-1088 cm ؊1 . These modes, also identified in Cu,Zn-SOD by using 15 N labeling, showed that the electronic properties of the histidine N ligands of copper are mostly affected upon copper reduction. A striking conclusion of this work is that peptide groups from loops and ␤-sheet largely participate in charge redistribution upon copper reduction, and in contrast, electronic properties of polar and charged amino acids of the superoxide access channel remain unaffected. This is notably shown for the strictly conserved Arg-143 by site-directed mutagenesis on chloroplastic Cu,Zn-SOD. Charge compensation by the peptide backbone and preserved electronic properties of the superoxide access channel and docking site upon copper reduction may be the determinant factors for the high reaction kinetics of superoxide with both reduced and oxidized Cu,Zn-SOD.

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Secondary structure dependent on metal ions of copper,zinc superoxide dismutase investigated by Fourier transform IR spectroscopy

et al. 1997

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Copper,zinc superoxide dismutase (Cu2Zn2‐SOD) from bovine erythrocyte and its metal ion free derivatives, E2Zn2‐SOD, Cu2E2‐SOD, and E2E2‐SOD (E: empty) were prepared and their secondary structures were investigated by Fourier transform ir spectroscopy. In 20 m M deuterated phosphate buffer (pD 7.5) solution at room temperature, the native Cu2Zn2‐SOD contains about 34% β‐strand, 17% β‐turn, and 49% unordered structures, which is similar to the content determined by x‐ray crystal structural analysis. The metal ion free derivatives decrease the component of β‐strand and increase the unordered structure component in trend. Especially in the cases of zinc‐free derivatives, Cu2E2‐SOD and E2E2‐SOD, about 24% β‐strand, 20% β‐turn, and 57% unordered structures are obtained. The result indicates that the zinc ion plays an important role in determining the secondary structure of copper,zinc superoxide dismutase. © 1997 John Wiley & Sons, Inc. Biopoly 42: 297–303, 1997

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Crystal structure of yeast Cu,Zn superoxide dismutase

Cited by 113 publications

References 45 publications

Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 Å resolution

Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 Å resolution

Long Distance Charge Redistribution Upon Cu,Zn-Superoxide Dismutase Reduction

Secondary structure dependent on metal ions of copper,zinc superoxide dismutase investigated by Fourier transform IR spectroscopy

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