REFINEMENT OF THE CRYSTAL-STRUCTURE OF RIBONUCLEASE-S - COMPARISON WITH AND BETWEEN THE VARIOUS RIBONUCLEASE-A STRUCTURES

被引:126
作者
KIM, EE [1 ]
VARADARAJAN, R [1 ]
WYCKOFF, HW [1 ]
RICHARDS, FM [1 ]
机构
[1] YALE UNIV,DEPT MOLEC BIOPHYS & BIOCHEM,NEW HAVEN,CT 06511
关键词
D O I
10.1021/bi00164a004
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
Ribonuclease S (RNase-S) is a complex that consists of two proteolytic fragments of bovine pancreatic ribonuclease A (RNase-A): the S-peptide (residues 1-20) and S-protein (residues 21-124). We have refined the crystal structures of three RNase-S complexes. The first two contain the full-length 20-residue S-peptide and were studied at pHs of 4.75 and 5.5. The third one consists of a truncated form of S-peptide (residues 1-15) and was studied at pH 4.75 as the reference structure for a series of mutant peptide complexes to be reported separately. Excluding residues 16-23 which are either missing (in the S15 complex) or disordered (in both S20 complexes), all three structures refined at 1.6-angstrom resolution are identical within the estimated errors in the coordinates (0.048 angstrom for the backbone atoms). The R-values, residual error, range from 17.4% to 18.6%. The final model of S20, pH 4.75, includes 1 sulfate and 84 water molecules. The side chains of 11 residues were modeled in two discrete conformations. The final structures were independent of the particular RNase-A or RNase-S used as a starting model. An extensive comparison with refined crystal structures of RNase-A reveals that the core of the molecule which is held together with extensive hydrogen bonds is in identical pattern in all cases. However, the loop regions vary from one structure to another and are often characterized by high B-factors. The pattern of thermal parameters appears to be dependent on crystal packing and correlates well with the accessibility calculated in the crystal. Gln60 is a conserved residue in all sequences known to date for this class of ribonucleases. However, it is the only residue that is clearly defined in an unfavorable position (phi = -100-degrees, psi = -130-degrees) on the Ramachandran plot. The origin of the substantial differences between RNase-A and RNase-S in stability to both acid and temperature denaturation and in susceptibility to proteolysis at neutral pH is not obvious in our visual comparison of these two structures.
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页码:12304 / 12314
页数:11
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共 57 条
  • [1] ACTION OF TRYPSIN ON RIBONUCLEASE-S
    ALLENDE, JE
    RICHARDS, FM
    [J]. BIOCHEMISTRY, 1962, 1 (02) : 295 - &
  • [2] MOLECULAR EVOLUTION OF THE RIBONUCLEASE SUPERFAMILY
    BEINTEMA, JJ
    SCHULLER, C
    IRIE, M
    CARSANA, A
    [J]. PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 1988, 51 (03) : 165 - 192
  • [3] BERSTEIN FC, 1977, J MOL BIOL, V112, P535
  • [4] CORRELATION BETWEEN OCCUPANCY AND TEMPERATURE FACTORS OF SOLVENT MOLECULES IN CRYSTAL-STRUCTURES OF PROTEINS
    BHAT, TN
    [J]. ACTA CRYSTALLOGRAPHICA SECTION A, 1989, 45 : 145 - 146
  • [5] Blackburn P, 1982, ENZYMES, VXV, P317
  • [6] BLEVINS RA, 1985, J BIOL CHEM, V260, P4264
  • [7] NUCLEAR MAGNETIC-RESONANCE AND NEUTRON-DIFFRACTION STUDIES OF THE COMPLEX OF RIBONUCLEASE-A WITH URIDINE VANADATE, A TRANSITION-STATE ANALOG
    BORAH, B
    CHEN, CW
    EGAN, W
    MILLER, M
    WLODAWER, A
    COHEN, JS
    [J]. BIOCHEMISTRY, 1985, 24 (08) : 2058 - 2067
  • [8] RIBONUCLEASE-A - LEAST-SQUARES REFINEMENT OF THE STRUCTURE AT 1.45 A RESOLUTION
    BORKAKOTI, N
    MOSS, DS
    PALMER, RA
    [J]. ACTA CRYSTALLOGRAPHICA SECTION B-STRUCTURAL SCIENCE, 1982, 38 (AUG): : 2210 - 2217
  • [9] Brtinger A. T., 1990, X PLOR VERSION 2 1
  • [10] CRYSTALLOGRAPHIC REFINEMENT BY SIMULATED ANNEALING - APPLICATION TO CRAMBIN
    BRUNGER, AT
    KARPLUS, M
    PETSKO, GA
    [J]. ACTA CRYSTALLOGRAPHICA SECTION A, 1989, 45 : 50 - 61