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PDBsum entry 1cf5
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Ribosome-inactivating protein
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PDB id
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1cf5
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Three-Dimensional structure of beta-Momorcharin at 2.55 a resolution.
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Authors
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Y.R.Yuan,
Y.N.He,
J.P.Xiong,
Z.X.Xia.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1999,
55,
1144-1151.
[DOI no: ]
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PubMed id
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Abstract
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Beta-Momorcharin (Mr approximately 29 kDa) is a single-chained
ribosome-inactivating protein (RIP) with a branched hexasaccharide bound to
Asn51. The crystal structure of beta-momorcharin has been determined using the
molecular-replacement method and refined to 2. 55 A resolution. The final
structural model gave an R factor of 17. 2% and root-mean-square deviations of
0.016 A and 1.76 degrees from ideal bond lengths and bond angles, respectively.
beta-Momorcharin contains nine alpha-helices, two 310 helices and three
beta-sheets, and its overall structure is similar to those of other
single-chained RIPs. Residues Tyr70, Tyr109, Glu158 and Arg161 are expected to
define the active site of beta-momorcharin as an rRNA N-glycosidase. The
oligosaccharide is linked to the protein through an N-glycosidic bond,
beta-GlcNAc-(1-N)-Asn51, and stretches from the surface of the N-terminal domain
far from the active site, which suggests that it should not play a role in
enzymatic function. The oligosaccharide of each beta-momorcharin molecule
interacts with the protein through hydrogen bonds, although in the crystals most
of these are intermolecular interactions with the protein atoms in an adjacent
unit cell. This is the first example of an RIP structure which provides
information about the three-dimensional structure and binding site of the
oligosaccharide in the active chains of RIPs.
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Figure 1.
Figure 1 Stereoscopic view of the (2F[o] - F[c]) electron
density of the six-stranded  -sheet
(molecule A) contoured at 1.0  .
This diagram was prepared using the molecular-graphics program
TURBO-FRODO.
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Figure 5.
Figure 5 Stereoscopic diagrams of the oligosaccharide structure
in [284][beta] -MMC, prepared using the molecular-graphics
program TURBO-FRODO. (a) The (2F[o] - F[c]) electron density of
the oligosaccharide of molecule A, contoured at 0.8 [285][sigma]
. Asn51 is also shown. (b) The (2F[o] - F[c]) electron density
of the oligosaccharide of molecule B, contoured at 0.8
[286][sigma] . Asn51 is also shown. (c) The superimposed
oligosaccharides of molecule A (in blue) and molecule B (in
red). (d) Interactions of the oligosaccharide (in blue) of
molecule A with the protein. Asn51 of molecule A is shown in
yellow; Glu110, Asn188-Glu189 and the C-terminus (Asn249) of
molecule #A are shown in red. The N-glycosidic bond is shown as
a solid line and the hydrogen bonds are shown as dashed lines.
(e) Interactions of the oligosaccharide (in blue) of molecule B
with the protein. Asn51 and Asn3 of molecule B are shown in
yellow; Gln189 and Asn209 of molecule #B are shown in red. The
N-glycosidic bond is shown as a solid line and the hydrogen
bonds are shown as dashed lines.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(1999,
55,
1144-1151)
copyright 1999.
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Secondary reference #1
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Title
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The determination and refinement of three-Dimensional structure of beta- Momorcharin at 2.4 a resolution
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Authors
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Y.-R.Yuan,
J.-P.Xiong,
Z.-X.Xia.
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Ref.
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chin chem lett, 1995,
6,
1053.
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Secondary reference #2
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Title
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Crystallization and preliminary crystallographic study of beta-Momorcharin.
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Authors
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J.P.Xiong,
Z.X.Xia,
L.Zhang,
G.J.Ye,
S.W.Jin,
Y.Wang.
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Ref.
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J Mol Biol, 1994,
238,
284-285.
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PubMed id
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