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PDBsum entry 1bc4
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References listed in PDB file
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Key reference
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Title
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The solution structure of a cytotoxic ribonuclease from the oocytes of rana catesbeiana (bullfrog).
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Authors
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C.F.Chang,
C.Chen,
Y.C.Chen,
K.Hom,
R.F.Huang,
T.H.Huang.
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Ref.
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J Mol Biol, 1998,
283,
231-244.
[DOI no: ]
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PubMed id
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Abstract
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RC-RNase is a pyrimidine-guanine sequence-specific ribonuclease and a lectin
possessing potent cell cytotoxicity. It was isolated from the oocytes of Rana
catesbeiana (bull frog). From analysis of an extensive set of 1H homonuclear 2D
NMR spectra we have completed the resonance assignments. Determination of the
three-dimensional structure was carried out with the program X-PLOR using a
total of 951 restraints including 814 NMR-derived distances, 61 torsion angles,
and 76 hydrogen bond restraints. In the resultant family of 15 best structures,
selected from a total of 150 calculated structures, the root-mean-square
deviation from the average structure for the backbone heavy-atoms involved in
well-defined secondary structure is 0.48 A, while that for all backbone
heavy-atoms is 0.91 A. The structure of RC-RNase consists of three alpha-helices
and two triple-stranded anti-parallel beta-sheets and folds in a kidney-shape,
very similar to the X-ray crystal structure of a homolo gous protein, onconase
isolated from Rana pipiens. We have also investigated the interaction between
RC-RNase and two inhibitors, cytidylyl(2'-->5')guanosine (2',5'-CpG) and
2'-deoxycytidylyl(3'-->5')-2'-deoxyguanosine (3',5'-dCpdG). Based on the
ligand-induced chemical shift changes in RC-RNase and the NOE cross-peaks
between RC-RNase and the inhibitors, the key residues involved in
protein-inhibitor interaction have been identified. The inhibitors were found to
bind in a "retro-binding" mode, with the guanine base bonded to the B1
subsite. The His103 residue was found to occupy the B state with the imidazole
ring pointing away from the active site. The structure coordinates and the NMR
restraints have been deposited in the Brookhaven Protein Data Bank (1bc4 and
1bc4mr, respectively).
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Figure 7.
Figure 7. The surface structure and surface charge profile
of the energy minimized, averaged structure of RC-RNase. The
structure was generated with the program GRASP [Nicholls et al
1991] with partial charge taken directly from the default charge
table (full.crg). Blue represents positive electrostatic
potential, red represents negative electrostatic potential and
white indicates charge neutral regions.
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Figure 9.
Figure 9. Spatial arrangement of the residues whose proton
chemical shifts change upon binding of 2',5'-CpG. These residues
are labeled and are shown by van der Waals spheres.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1998,
283,
231-244)
copyright 1998.
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Secondary reference #1
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Title
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The secondary structure of a pyrimidine-Guanine sequence-Specific ribonuclease possessing cytotoxic activity from the oocytes of rana catesbeiana.
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Authors
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C.Chen,
K.Hom,
R.F.Huang,
P.J.Chou,
Y.D.Liao,
T.Huang.
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Ref.
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J Biomol Nmr, 1996,
8,
331-344.
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PubMed id
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