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PDBsum entry 1jbt
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Hydrolase/RNA
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PDB id
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1jbt
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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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Crystal structures of restrictocin-Inhibitor complexes with implications for RNA recognition and base flipping.
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Authors
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X.Yang,
T.Gérczei,
L.T.Glover,
C.C.Correll.
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Ref.
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Nat Struct Biol, 2001,
8,
968-973.
[DOI no: ]
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PubMed id
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Abstract
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The cytotoxin sarcin disrupts elongation factor binding and protein synthesis by
specifically cleaving one phosphodiester bond in ribosomes. To elucidate the
molecular basis of toxin action, we determined three cocrystal structures of the
sarcin homolog restrictocin bound to different analogs that mimic the target
sarcin/ricin loop (SRL) structure of the rat 28S rRNA. In these structures,
restrictocin contacts the bulged-G motif and an unfolded form of the tetraloop
of the SRL RNA. In one structure, toxin loops guide selection of the target site
by contacting the base critical for recognition (G4319) and the surrounding
S-shaped backbone. In another structure, base flipping of the tetraloop enables
cleavage by placing the target nucleotide in the active site with the
nucleophile nearly inline for attack on the scissile bond. These structures
provide the first views of how a site-specific protein endonuclease recognizes
and cleaves a folded RNA substrate.
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Figure 1.
Figure 1. Structural overview. a, Schematic of the RNA
sequence showing the conserved nucleotides (boxed), tetraloop
(green) and bulged-G motif (yellow). The sites of 2'
modification of the stem (asterisks) and of 4325 and 4326 (plus
signs) are shown. The terminal nucleotides are designed to pair
and create a blunt end (red); the remainder corresponds to rat
28S nucleotides 4315 -4333 (hereafter, Escherichia coli 23S
numbering is in parentheses). The two 29-mer variants
(nU4325dA^4326 and mG4325dA^4326) are missing the first and the
last nucleotide. When enzyme concentrations exceed that of
substrates other than ribosomes, cleavage by the toxin is
primarily on the 3' side of purines3. b, A ribbon drawing of the
restrictocin -mG4325 (misdocked) complex showing the tetraloop
(green) and bulged-G motif (yellow) of the substrate, as well as
the bound potassium ions (pink).
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Figure 4.
Figure 4. Implications for cleavage and recognition. a,
Superposition of the structure of the scissile phosphate groups
of the target nucleotide from the uncomplexed substrate SRL
RNA^11 (red), the 3' splice site of a splicing endonuclease^19
(yellow) and the ground state forms of the lead-dependent22
(navy) and the hammerhead^20 (blue) ribozymes. b, Superposition
of the structures of the two types of S-turn: one in the bound
complex (blue) and another in the L11 -RNA complex38 (yellow).
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Biol
(2001,
8,
968-973)
copyright 2001.
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