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PDBsum entry 2b51
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Transferase/RNA binding protein
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PDB id
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2b51
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References listed in PDB file
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Key reference
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Title
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Structural basis for utp specificity of RNA editing tutases from trypanosoma brucei.
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Authors
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J.Deng,
N.L.Ernst,
S.Turley,
K.D.Stuart,
W.G.Hol.
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Ref.
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EMBO J, 2005,
24,
4007-4017.
[DOI no: ]
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PubMed id
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Abstract
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Trypanosomatids are pathogenic protozoa that undergo a unique form of
post-transcriptional RNA editing that inserts or deletes uridine nucleotides in
many mitochondrial pre-mRNAs. Editing is catalyzed by a large multiprotein
complex, the editosome. A key editosome enzyme, RNA editing terminal uridylyl
transferase 2 (TUTase 2; RET2) catalyzes the uridylate addition reaction. Here,
we report the 1.8 A crystal structure of the Trypanosoma brucei RET2 apoenzyme
and its complexes with uridine nucleotides. This structure reveals that the
specificity of the TUTase for UTP is determined by a crucial water molecule that
is exquisitely positioned by the conserved carboxylates D421 and E424 to sense a
hydrogen atom on the N3 position of the uridine base. The three-domain structure
also unveils a unique domain arrangement not seen before in the
nucleotidyltansferase superfamily, with a large domain insertion between the
catalytic aspartates. This insertion is present in all trypanosomatid TUTases.
We also show that TbRET2 is essential for survival of the bloodstream form of
the parasite and therefore is a potential target for drug therapy.
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Figure 3.
Figure 3 Overall structure of TbRET2. (A) Ribbon presentation of
the molecule. The three domains are shown in green (NTD), yellow
(MD) and blue (CTD) (as in Figure 1). The UTP-Mg2+ at site A is
shown as ball-and-stick in a cleft between the NTD and the CTD.
(B-D) Electrostatic potential surface of TbRET2. The positive
and negative regions are colored in blue and red, respectively.
Nucleotide-binding sites are labeled in yellow. UTP/UMP and Mg2+
are shown as ball-and-stick. Notice the extended blue patch
across three domains that suggests an RNA binding region. (B)
Front view, UTP-binding site A with a UTP and nucleotide-binding
site B with a UMP molecule; (C) side view (90° upward rotation),
nucleotide-binding site B with a UMP molecule; (D) back view
(180° upward rotation), nucleotide-binding site C with a UMP
molecule. Figure generated by PYMOL (DeLano, 2002).
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Figure 5.
Figure 5 UTP-specificity and UMP binding. (A) Interactions of
the UTP sugar moiety at site A with the 2'-OH and the side
chains of N277 and S278. (B) The uridine base is specifically
recognized by Wat1 and D421 and E424. The two hydrogen atoms of
Wat1 shown as white spheres makes exquisite hydrogen bonds with
O   1
of D421 and O  epsilon
1 of E424. The latter two residues are conserved among all
trypanosomatid TUTases (Figure 1). (C) UMP binding at site B;
(D) UMP binding at site C, which is located far from the active
site.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
EMBO J
(2005,
24,
4007-4017)
copyright 2005.
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