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PDBsum entry 1ahb
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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 n-Glycosidase mechanism of ribosome-Inactivating proteins implied by crystal structures of alpha-Momorcharin.
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Authors
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J.Ren,
Y.Wang,
Y.Dong,
D.I.Stuart.
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Ref.
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Structure, 1994,
2,
7.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: alpha-Momorcharin (alpha MMC) is a type I ribosome-inactivating
protein. It inhibits protein synthesis by hydrolytically removing a specific
adenine residue from a highly conserved, single-stranded loop of rRNA. RESULTS:
Here we describe the determination and refinement of the crystal structures of
alpha MMC in the native state and in complexes with the product, adenine, and a
substrate analogue, formycin 5'-monophosphate (FMP) at high resolution. Both
adenine and the base of FMP are tightly bound; the ribose of bound FMP adopts a
strained, high-energy conformation, which may mimic the structure of the
transition state. CONCLUSIONS: These structures indicate that residues Tyr70,
Glu160 and Arg163 of alpha MMC are the most critical for catalysis. We propose
that the strained conformation of the ribose in the target adenosine weakens the
glycoside bond. Partial protonation mediated by Arg163 then facilitates
N-glycoside bond cleavage, leading to the formation of an oxycarbonium ion
intermediate which is stabilized by the negatively-charged Glu160. Tyr70 adopts
subtly different conformations in the three structures implying that it may be
important in substrate recognition and perhaps catalysis.
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Figure 3.
Figure 3. Schematic ribbon representation of the αMMC molecule
as viewed towards the active site cleft. The bound FMP molecule
is shown in a stick representation. The secondary structural
elements are: α[1], 11– 23; α[2], 86–91; α[3],
111–118; α[4], 129–139; α[5], 144–163; α[6], 165–173;
α[7], 183–191; α[8], 192–202; α[9], 231–234; β[1],
3–5; β[2], 27–31; β[3], 34–37; β[4], 47–53; β[5],
59–65; β[6], 70–76; β[7], 79–82; β[8], 101–104;
β[9], 208–215; β[10], 223–227. Figure 3. Schematic
ribbon representation of the αMMC molecule as viewed towards
the active site cleft. The bound FMP molecule is shown in a
stick representation. The secondary structural elements are:
α[1], 11– 23; α[2], 86–91; α[3], 111–118; α[4],
129–139; α[5], 144–163; α[6], 165–173; α[7], 183–191;
α[8], 192–202; α[9], 231–234; β[1], 3–5; β[2],
27–31; β[3], 34–37; β[4], 47–53; β[5], 59–65; β[6],
70–76; β[7], 79–82; β[8], 101–104; β[9], 208–215;
β[10], 223–227.
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Figure 5.
Figure 5. A schematic diagram showing the mechanism of
N-glycoside bond hydrolysis catalyzed by αMMC. Hydrogen bonding
at N3 and N1 by Arg163 and Ile71, respectively, facilitates the
cleavage of the glycoside bond (N9–C1′ ) and leads to the
formation of a transition state with oxycarbonium ion
development on the ribose. The oxycarbonium ion is then
stabilized by the negative charge of Glu160. The adenine ring
rotates by about 15° to the position found in the
adenine-bound structures to give enough space for the
OH^−of the nucleophile to bond to C1′. Meanwhile, movement
and conformational change of the ribose may occur because of the
release of the straining force after the N9–C1′ bond is
broken. A water molecule, OH0 or OH2, attacks the oxycarbonium
ion at C1′ and the proton is transferred to N9. Figure 5. A
schematic diagram showing the mechanism of N-glycoside bond
hydrolysis catalyzed by αMMC. Hydrogen bonding at N3 and N1 by
Arg163 and Ile71, respectively, facilitates the cleavage of the
glycoside bond (N9–C1′ ) and leads to the formation of a
transition state with oxycarbonium ion development on the
ribose. The oxycarbonium ion is then stabilized by the negative
charge of Glu160. The adenine ring rotates by about 15° to
the position found in the adenine-bound structures to give
enough space for the OH^−of the nucleophile to bond to
C1′. Meanwhile, movement and conformational change of the
ribose may occur because of the release of the straining force
after the N9–C1′ bond is broken. A water molecule, OH0 or
OH2, attacks the oxycarbonium ion at C1′ and the proton is
transferred to N9.
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The above figures are
reprinted
by permission from Cell Press:
Structure
(1994,
2,
7-0)
copyright 1994.
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Secondary reference #1
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Title
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Molecular replacement studies of alpha-Momorcharin (in: proceedings of the ccp4 study weekend: molecular replacement, Edited by e.J.Dodson, S.Gover,W.Wolf)
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Authors
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J.Ren,
Y.Wang,
Y.Dong,
D.I.Stuart.
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Ref.
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daresbury lab [rep ]dlscir, 1992,
33,
116.
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Secondary reference #2
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Title
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Crystals of alpha-Momorcharin, A new ribosome-Inactivating protein
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Authors
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Z.Feng,
W.W.Li,
H.W.Yeung,
S.Chen,
Y.Wang,
X.Lin,
Y.Dong,
J.Wang.
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Ref.
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j mol biol, 1990,
214,
625.
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