Crystal structure of Escherichia coli manganese superoxide dismutase at 2.1-Å resolution

被引:133
作者
Edwards, RA
Baker, HM
Whittaker, MM
Whittaker, JW
Jameson, GB
Baker, EN [1 ]
机构
[1] Massey Univ, Dept Biochem, Palmerston North, New Zealand
[2] Massey Univ, Dept Chem, Palmerston North, New Zealand
[3] Oregon Grad Inst, Dept Biochem & Mol Biol, Portland, OR 97291 USA
来源
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY | 1998年 / 3卷 / 02期
基金
美国国家卫生研究院;
关键词
superoxide dismutase; manganese enzyme; crystal structure; metalloprotein; DNA binding;
D O I
10.1007/s007750050217
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The three-dimensional structure of the manganese-dependent superoxide dismutase (MnSOD) from Escherichia coli has been determined by X-ray crystallography at 2.1 Angstrom resolution The protein crystallizes with two homodimers in the asymmetric unit, and a model comprising 6528 protein atoms (residues 1-205 of all four monomers), four manganese ions and 415 water molecules has been refined to an R factor of 0.188 (R-free 0.218). The structure shows a high degree of similarity with other MnSOD and FeSOD enzymes. The Mn centres are 5-coordinate, trigonal bipyramidal, with His26 and a solvent molecule, probably a hydroxide ion, as apical ligands, and His81, Asp167 and His171 as equatorial ligands. The coordinated solvent molecule is linked to a network of hydrogen bonds involving the non-coordinated carboxylate oxygen of Asp167 and a conserved glutamine residue, Gln146. The MnSOD dimer is notable for the way in which the two active sites are interconnected and a "bridge" comprising His171 of one monomer and Glu170 of the other offers a route for inter-site communication. Comparison of E. coli MnSOD and FeSOD (a) reveals some differences in the dimer interface, (b) yields no obvious explanation for their metal specificities, and (c) provides a structural basis for differences in DNA binding, where for MnSOD the groove formed by dimerization is complementary in charge and surface contour to B-DNA.
引用
收藏
页码:161 / 171
页数:11
相关论文
共 54 条
[1]   OXIDATIVE DAMAGE TO DNA - RELATION TO SPECIES METABOLIC-RATE AND LIFE-SPAN [J].
ADELMAN, R ;
SAUL, RL ;
AMES, BN .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1988, 85 (08) :2706-2708
[2]   CHARACTERIZATION OF SUPEROXIDE DISMUTASES PURIFIED FROM EITHER ANAEROBICALLY MAINTAINED OR AERATED BACTEROIDES-GINGIVALIS [J].
AMANO, A ;
SHIZUKUISHI, S ;
TAMAGAWA, H ;
IWAKURA, K ;
TSUNASAWA, S ;
TSUNEMITSU, A .
JOURNAL OF BACTERIOLOGY, 1990, 172 (03) :1457-1463
[3]   DIETARY CARCINOGENS AND ANTICARCINOGENS - OXYGEN RADICALS AND DEGENERATIVE DISEASES [J].
AMES, BN .
SCIENCE, 1983, 221 (4617) :1256-1264
[4]  
[Anonymous], TURBO FRODO SILICON
[5]   MANGANESE SUPEROXIDE DISMUTASES FROM ESCHERICHIA-COLI AND FROM YEAST MITOCHONDRIA - PRELIMINARY X-RAY CRYSTALLOGRAPHIC STUDIES [J].
BEEM, KM ;
RICHARDSON, JS ;
RICHARDSON, DC .
JOURNAL OF MOLECULAR BIOLOGY, 1976, 105 (02) :327-332
[6]  
BEYER W, 1991, PROG NUCLEIC ACID RE, V40, P221
[7]   DIFFERENCES BETWEEN THE MANGANESE-CONTAINING AND THE IRON-CONTAINING SUPEROXIDE DISMUTASES OF ESCHERICHIA-COLI DETECTED THROUGH SEDIMENTATION EQUILIBRIUM, HYDRODYNAMIC, AND SPECTROSCOPIC STUDIES [J].
BEYER, WF ;
REYNOLDS, JA ;
FRIDOVICH, I .
BIOCHEMISTRY, 1989, 28 (10) :4403-4409
[8]   THE STRUCTURE OF HUMAN MITOCHONDRIAL MANGANESE SUPEROXIDE-DISMUTASE REVEALS A NOVEL TETRAMERIC INTERFACE OF 2 4-HELIX BUNDLES [J].
BORGSTAHL, GEO ;
PARGE, HE ;
HICKEY, MJ ;
BEYER, WF ;
HALLEWELL, RA ;
TAINER, JA .
CELL, 1992, 71 (01) :107-118
[9]   X-RAY STRUCTURE-ANALYSIS OF THE IRON-DEPENDENT SUPEROXIDE-DISMUTASE FROM MYCOBACTERIUM-TUBERCULOSIS AT 2.0-ANGSTROMS RESOLUTION REVEALS NOVEL DIMER-DIMER INTERACTIONS [J].
COOPER, JB ;
MCINTYRE, K ;
BADASSO, MO ;
WOOD, SP ;
ZHANG, Y ;
GARBE, TR ;
YOUNG, D .
JOURNAL OF MOLECULAR BIOLOGY, 1995, 246 (04) :531-544
[10]   THE DOUBLE CUBIC LATTICE METHOD - EFFICIENT APPROACHES TO NUMERICAL-INTEGRATION OF SURFACE-AREA AND VOLUME AND TO DOT SURFACE CONTOURING OF MOLECULAR ASSEMBLIES [J].
EISENHABER, F ;
LIJNZAAD, P ;
ARGOS, P ;
SANDER, C ;
SCHARF, M .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 1995, 16 (03) :273-284