1XSO

THREE-DIMENSIONAL STRUCTURE OF XENOPUS LAEVIS CU,ZN SUPEROXIDE DISMUTASE B DETERMINED BY X-RAY CRYSTALLOGRAPHY AT 1.5 ANGSTROMS RESOLUTION

Summary for 1XSO

• Entry DOI: 10.2210/pdb1xso/pdb
• Descriptor: COPPER,ZINC SUPEROXIDE DISMUTASE, COPPER (II) ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: oxidoreductase (superoxide acceptor)
• Biological source: Xenopus laevis (African clawed frog)
• Total number of polymer chains: 2
• Total formula weight: 30871.66

Authors

Djinovic Carugo, K.,Coda, A.,Battistoni, A.,Carri, M.T.,Polticelli, F.,Desideri, A.,Rotilio, G.,Wilson, K.S.,Bolognesi, M. (deposition date: 1995-03-14, release date: 1995-07-10, Last modification date: 2019-08-14)

Primary citation

Djinovic Carugo, K.,Battistoni, A.,Carri, M.T.,Polticelli, F.,Desideri, A.,Rotilio, G.,Coda, A.,Wilson, K.S.,Bolognesi, M.
Three-dimensional structure of Xenopus laevis Cu,Zn superoxide dismutase b determined by X-ray crystallography at 1.5 A resolution.
Acta Crystallogr.,Sect.D, 52:176-188, 1996

PubMed Abstract: Xenopus laevis Cu,Zn superoxide dismutase (recombinant isoenzyme b) has been crystallized and the structure determined at 1.49 A resolution. The crystals belong to space group P2(1)2(1)2(1), with cell constants a = 73.33, b = 68.86, c = 59.73 A, and contain one dimeric molecule of M(r) 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 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 0.036 A. 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 (beta-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.

PubMed: 15299740
DOI: 10.1107/S0907444995007608

Experimental method

X-RAY DIFFRACTION (1.49 Å)