REFINED CRYSTAL-STRUCTURE OF CD, ZN METALLOTHIONEIN AT 2.0 A RESOLUTION

被引:266
作者
ROBBINS, AH
MCREE, DE
WILLIAMSON, M
COLLETT, SA
XUONG, NH
FUREY, WF
WANG, BC
STOUT, CD
机构
[1] Scripps Res Inst, RES INST, DEPT MOLEC BIOL, LA JOLLA, CA 92037 USA
[2] UNIV CALIF SAN DIEGO, DEPT CHEM, LA JOLLA, CA 92093 USA
[3] UNIV CALIF SAN DIEGO, DEPT PHYS, LA JOLLA, CA 92093 USA
[4] UNIV CALIF SAN DIEGO, DEPT BIOL, LA JOLLA, CA 92093 USA
[5] VET ADM MED CTR, BIOCRYSTALLOG LAB, PITTSBURGH, PA 15240 USA
[6] UNIV PITTSBURGH, DEPT CRYSTALLOG, PITTSBURGH, PA 15260 USA
关键词
DIRECT METHODS; METAL-SULFUR CLUSTERS; CYSTEINE THIOLATE LIGANDS;
D O I
10.1016/0022-2836(91)90933-W
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 crystal structure of Cd5,Zn2-metallothionein from rat liver has been refined at 2.0 Å resolution of a R-value of 0.176 for all observed data. The five Cd positions in the asymmetric unit of the crystal create a pseudo-centrosymmetric constellation about a crystallographic 2-fold axis. Consequently, the distribution of anomalous differences is almost ideally centrosymmetric. Therefore, the previously reported metal positions and the protein model derived therefrom are incorrect. Direct methods were applied to the protein amplitudes to locate the Cd positions. The new positions were used to calculate a new electron density map based on the Cd anomalous scattering and partial structure to model the metal clusters and the protein. Phases calculated from this model predict the positions of three sites in a (NH4)2WS4 derivative. Single isomorphous replacement phases calculated with these tungsten sites confirm the positions of the Cd sites from the new direct methods calculations. The refined metallothionein structure has a root-mean-square deviation of 0.016 Å from ideality of bonds and normal stereochemistry of φ, θ{symbol} and χ torsion angles. The metallothionein crystal structure is in agreement with the structures for the α and β domains in solution derived by nuclear magnetic resonance methods. The overall chain folds and all metal to cysteine bonds are the same in the two structure determinations. The handedness of a short helix in the α-domain (residues 41 to 45) is the same in both structures. The crystal structure provides information concerning the metal cluster geometry and cysteine solvent accessibility and side-chain stereochemistry. Short cysteine peptide sequences repeated in the structure adopt restricted conformations which favor the formation of amide to sulfur hydrogen bonds. The crystal packing reveals intimate association of molecules about the diagonal 2-fold axes and trapped ions of crystallization (modeled as phosphate and sodium). Variation in the chemical and structural environments of the metal sites is in accord with data for metal exchange reactions in metallothioneins. © 1991.
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页码:1269 / 1293
页数:25
相关论文
共 61 条
  • [1] STRUCTURAL STUDY OF THE COPPER AND ZINC SITES IN METALLOTHIONEINS BY USING EXTENDED X-RAY-ABSORPTION FINE-STRUCTURE
    ABRAHAMS, IL
    BREMNER, I
    DIAKUN, GP
    GARNER, CD
    HASNAIN, SS
    ROSS, I
    VASAK, M
    [J]. BIOCHEMICAL JOURNAL, 1986, 236 (02) : 585 - 589
  • [2] ADMAN E, 1975, P NATL ACAD SCI USA, V72, P4854, DOI 10.1073/pnas.72.12.4854
  • [3] 3-DIMENSIONAL STRUCTURE OF RABBIT LIVER [CD7]METALLOTHIONEIN-2A IN AQUEOUS-SOLUTION DETERMINED BY NUCLEAR MAGNETIC-RESONANCE
    ARSENIEV, A
    SCHULTZE, P
    WORGOTTER, E
    BRAUN, W
    WAGNER, G
    VASAK, M
    KAGI, JHR
    WUTHRICH, K
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1988, 201 (03) : 637 - 657
  • [4] CADMIUM BINDING AND METAL CLUSTER FORMATION IN METALLOTHIONEIN - A DIFFERENTIAL MODIFICATION STUDY
    BERNHARD, WR
    VASAK, M
    KAGI, JHR
    [J]. BIOCHEMISTRY, 1986, 25 (08) : 1975 - 1980
  • [5] PROTEIN DATA BANK - COMPUTER-BASED ARCHIVAL FILE FOR MACROMOLECULAR STRUCTURES
    BERNSTEIN, FC
    KOETZLE, TF
    WILLIAMS, GJB
    MEYER, EF
    BRICE, MD
    RODGERS, JR
    KENNARD, O
    SHIMANOUCHI, T
    TASUMI, M
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1977, 112 (03) : 535 - 542
  • [6] PROTON NMR-STUDIES OF THE COBALT(II)-METALLOTHIONEIN SYSTEM
    BERTINI, I
    LUCHINAT, C
    MESSORI, L
    VASAK, M
    [J]. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1989, 111 (19) : 7296 - 7300
  • [7] BOULANGER Y, 1982, J BIOL CHEM, V257, P13717
  • [8] CRYSTALLOGRAPHIC REFINEMENT BY SIMULATED ANNEALING - APPLICATION TO CRAMBIN
    BRUNGER, AT
    KARPLUS, M
    PETSKO, GA
    [J]. ACTA CRYSTALLOGRAPHICA SECTION A, 1989, 45 : 50 - 61
  • [9] COOPERATIVE CLUSTER FORMATION IN METALLOTHIONEIN
    BYRD, J
    WINGE, DR
    [J]. ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 1986, 250 (01) : 233 - 237
  • [10] GEOMETRY OF INTERACTION OF METAL-IONS WITH SULFUR-CONTAINING LIGANDS IN PROTEIN STRUCTURES
    CHAKRABARTI, P
    [J]. BIOCHEMISTRY, 1989, 28 (14) : 6081 - 6085