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

Kristina Djinović Carugo, Andrea Battistoni, Maria Teresa Carrì, Fabio Polticelli, Alessandro Desideri, Giuseppe Rotilio, Alessandro Coda, Keith S. Wilson, Martino Bolognesi

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Abstract

Xenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has been crystallized and the structure determined at 1.49 Å resolution. The crystals belong to space group P212121, with cell constants a = 73.33, b = 68.86, c = 59.73 Å, and contain one dimeric molecule of Mr 32 000 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 Å resolution range is 0.104, for a model comprising 2023 protein atoms, two Cu2+, two Zn2+, and 353 water molecules. The overall temperature factor for the model, including solvent, is 20.3 Å2, while the calculated r.m.s. coordinate error for the refined model is 0.036 Å. 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 β-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.

Original languageEnglish
Pages (from-to)176-188
Number of pages13
JournalActa Crystallographica Section D: Biological Crystallography
Volume52
Issue number1
Publication statusPublished - Jan 1 1996

Fingerprint

inorganic peroxides
X ray crystallography
X Ray Crystallography
Xenopus laevis
Superoxide Dismutase
crystallography
Isoenzymes
Hot Temperature
x rays
Water
R Factors
Molecules
Molecular Dynamics Simulation
Catalytic Domain
molecules
Metals
Atoms
homology
Temperature
Dimers

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Biochemistry
  • Biophysics
  • Clinical Biochemistry
  • Structural Biology
  • Condensed Matter Physics

Cite this

Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 Å resolution. / Carugo, Kristina Djinović; Battistoni, Andrea; Carrì, Maria Teresa; Polticelli, Fabio; Desideri, Alessandro; Rotilio, Giuseppe; Coda, Alessandro; Wilson, Keith S.; Bolognesi, Martino.

In: Acta Crystallographica Section D: Biological Crystallography, Vol. 52, No. 1, 01.01.1996, p. 176-188.

Research output: Contribution to journalArticle

Carugo, KD, Battistoni, A, Carrì, MT, Polticelli, F, Desideri, A, Rotilio, G, Coda, A, Wilson, KS & Bolognesi, M 1996, 'Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 Å resolution', Acta Crystallographica Section D: Biological Crystallography, vol. 52, no. 1, pp. 176-188.
Carugo, Kristina Djinović ; Battistoni, Andrea ; Carrì, Maria Teresa ; Polticelli, Fabio ; Desideri, Alessandro ; Rotilio, Giuseppe ; Coda, Alessandro ; Wilson, Keith S. ; Bolognesi, Martino. / Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 Å resolution. In: Acta Crystallographica Section D: Biological Crystallography. 1996 ; Vol. 52, No. 1. pp. 176-188.
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abstract = "Xenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has been crystallized and the structure determined at 1.49 {\AA} resolution. The crystals belong to space group P212121, with cell constants a = 73.33, b = 68.86, c = 59.73 {\AA}, and contain one dimeric molecule of Mr 32 000 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 {\AA} resolution range is 0.104, for a model comprising 2023 protein atoms, two Cu2+, two Zn2+, and 353 water molecules. The overall temperature factor for the model, including solvent, is 20.3 {\AA}2, while the calculated r.m.s. coordinate error for the refined model is 0.036 {\AA}. 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 β-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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AU - Carugo, Kristina Djinović

AU - Battistoni, Andrea

AU - Carrì, Maria Teresa

AU - Polticelli, Fabio

AU - Desideri, Alessandro

AU - Rotilio, Giuseppe

AU - Coda, Alessandro

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