1COB

CRYSTAL STRUCTURE SOLUTION AND REFINEMENT OF THE SEMISYNTHETIC COBALT SUBSTITUTED BOVINE ERYTHROCYTE ENZYME SUPEROXIDE DISMUTASE AT 2.0 ANGSTROMS RESOLUTION

1COB の概要

• エントリーDOI: 10.2210/pdb1cob/pdb
• 分子名称: SUPEROXIDE DISMUTASE, COPPER (II) ION, COBALT (II) ION, ... (4 entities in total)
• 機能のキーワード: oxidoreductase
• 由来する生物種: Bos taurus (cattle)
• 細胞内の位置: Cytoplasm: P00442
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 31391.63

構造登録者

Djinovic, K.,Coda, A.,Antolini, L.,Pelosi, G.,Desideri, A.,Falconi, M.,Rotilio, G.,Bolognesi, M. (登録日: 1992-02-19, 公開日: 1993-10-31, 最終更新日: 2024-10-23)

主引用文献

Djinovic, K.,Coda, A.,Antolini, L.,Pelosi, G.,Desideri, A.,Falconi, M.,Rotilio, G.,Bolognesi, M.
Crystal structure solution and refinement of the semisynthetic cobalt-substituted bovine erythrocyte superoxide dismutase at 2.0 A resolution.
J.Mol.Biol., 226:227-238, 1992

PubMed Abstract: The semisynthetic Co-substituted bovine erythrocyte superoxide dismutase (SOD) has been crystallized in a new crystalline form and the structure determined at 2.0 A (1 A = 0.1 nm) resolution. The crystals belong to space group P2(1)2(1)2(1) with cell constants: a = 51.0, b = 147.6, c = 47.5 A, and contain one dimeric molecule of 32,000 M(r) per asymmetric unit. The structure has been solved by molecular replacement techniques using the Cu,Zn bovine enzyme as a search model, and refined by molecular dynamics with the crystallographic pseudo-energy term, followed by conventional crystallographic refinement. The R-factor for the 18,964 unique reflections in the resolution range from 10.0 to 2.0 A is 0.176 for a model comprising 2188 protein atoms and 200 solvent molecules; the root-mean-square deviation from the ideal bond lengths is 0.010 A, and the average atomic temperature factor is 26.5 A2. The dimeric molecule of the enzyme is composed of two identical subunits related by a non-crystallographic 2-fold axis. The subunit has as its structural scaffolding the conventional SOD-flattened antiparallel eight-stranded beta-barrel, with three external loops. The co-ordination geometry of the metal center in the active site is fairly well preserved when compared with the native Cu,Zn bovine enzyme. Co2+ is in tetrahedral co-ordination, while the Cu2+ ligands show an uneven distortion from the square planar geometry. The least-squares superposition of the metals ligands and the catalytically important Arg141 of the native and Co-substituted enzyme yields a root-mean-square value of 0.401 A, the largest deviation occurring at the Co2+ ligand Asp81. An additional copper ligand, compatible with a water molecule, is observed at 2.38 A from Cu2+ in the active-site channel, at the supposed binding site of the O2- anion substrate. Several ordered water molecules have been observed on the protein surface and in the active-site channel; their structural locations coincide remarkably with those of related water molecules found in the crystal structure of the phylogenetically distant superoxide dismutase from yeast.

PubMed: 1619651
DOI: 10.1016/0022-2836(92)90135-7

実験手法

X-RAY DIFFRACTION (2 Å)