Three-dimensional structure of Cu,Zn-superoxide dismutase from spinach at 2.0 A resolution.
The three-dimensional structure of Cu,Zn-superoxide dismutase from spinach leaves has been determined by X-ray crystal structure analysis. The atomic coordinates were refined at 2.0 A resolution using the Hendrickson and Konnert program for stereochemically restrained refinement against structure factors, which allowed the use of non-crystallographic symmetry. The crystallographic residual error for the refined model was 24.9%, with a root mean square deviation of 0.03 A from the ideal bond length and an average atomic temperature factor of 9.6 A. A dimeric molecule of the enzyme is comprised of two identical subunits related by a non-crystallographic 2-fold axis. Each subunit of 154 amino acid residues is composed primarily of eight anti-parallel beta-strands that form a flattened cylinder, plus three external loops. The main-chain hydrogen bonds primarily link the beta-strands. The overall structure of this enzyme is quite similar to that of the bovine dismutase except for some parts. The single disulfide bridge (Cys57-Cys146) and the salt bridge (Arg79-Asp101) may stabilize the loop regions of the structure. The Cu2+ and Zn2+ ions in the active site lie 6.1 A apart at the bottom of the long channel. The Cu2+ ligands (ND1 of His-46, and NE2 of His-48, -63, and -120) show an uneven tetrahedral distortion from a square plane. The Zn2+ ligands (ND1 of His-63, -71, and -80 and OD1 of Asp-83) show an almost tetrahedral geometry. The imidazole ring of His-63 forms a bridge between the Cu2+ and Zn2+ ions.(ABSTRACT TRUNCATED AT 250 WORDS)
Kitagawa
Y
Y
Institute for Protein Research, Osaka University.
Tanaka
N
N
Hata
Y
Y
Kusunoki
M
M
Lee
G P
GP
Katsube
Y
Y
Asada
K
K
Aibara
S
S
Morita
Y
Y
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D003300:Copper / Q000737:chemistry; D004220:Disulfides / Q000737:chemistry; D006860:Hydrogen Bonding; D008024:Ligands; D008969:Molecular Sequence Data; D010944:Plants / Q000201:enzymology*; D011487:Protein Conformation; D013237:Stereoisomerism; D013482:Superoxide Dismutase / Q000737:chemistry*; D013696:Temperature; D014867:Water / Q000737:chemistry; D014961:X-Ray Diffraction; D015032:Zinc / Q000737:chemistry
D004220:Disulfides; D008024:Ligands; D014867:Water; D003300:Copper; D013482:Superoxide Dismutase; D015032:Zinc