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PDBsum entry 2ab5
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Protein binding
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PDB id
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2ab5
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References listed in PDB file
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Key reference
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Title
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Evolution from DNA to RNA recognition by the bi3 laglidadg maturase.
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Authors
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A.Longo,
C.W.Leonard,
G.S.Bassi,
D.Berndt,
J.M.Krahn,
T.M.Hall,
K.M.Weeks.
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Ref.
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Nat Struct Mol Biol, 2005,
12,
779-787.
[DOI no: ]
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PubMed id
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Abstract
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LAGLIDADG endonucleases bind across adjacent major grooves via a saddle-shaped
surface and catalyze DNA cleavage. Some LAGLIDADG proteins, called maturases,
facilitate splicing by group I introns, raising the issue of how a DNA-binding
protein and an RNA have evolved to function together. In this report,
crystallographic analysis shows that the global architecture of the bI3 maturase
is unchanged from its DNA-binding homologs; in contrast, the endonuclease active
site, dispensable for splicing facilitation, is efficiently compromised by a
lysine residue replacing essential catalytic groups. Biochemical experiments
show that the maturase binds a peripheral RNA domain 50 A from the splicing
active site, exemplifying long-distance structural communication in a
ribonucleoprotein complex. The bI3 maturase nucleic acid recognition saddle
interacts at the RNA minor groove; thus, evolution from DNA to RNA function has
been mediated by a switch from major to minor groove interaction.
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Figure 7.
Figure 7. Maturase-RNA interactions. (a) Site-directed
cleavage patterns superimposed on a three-dimensional model for
the bI3 maturase and P5-P4-P6 domain complex. Spheres, sites of
derivatization; colored RNA backbones, cleavage sites; green,
 -strands
of the bI3 maturase. (b) Summary of 2'-O-methyl interference in
the P5b and P5c helices. Maturase is shown slightly transparent
for clarity. Red spheres, sites of 2'-O-methyl interference
(Supplementary Fig. 1); blue backbone, solvent-based hydroxyl
radical cleavage sites (Fig. 5c,d).
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Figure 8.
Figure 8. Maturase-facilitated folding of the bI3 intron RNA via
action at a distance. The bI3 maturase recognizes a distal
structure in a peripheral domain and lies at least 50 Å from the
group I intron active site (orange). Green, the maturase -strands;
dark gray, the remainder of the protein; light blue, regions
protected from solvent-based hydroxyl radical cleavage upon
maturase binding; yellow spheres, sulfate groups visualized
crystallographically; brown asterisk, a potential auxiliary
RNA-protein interaction site.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2005,
12,
779-787)
copyright 2005.
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