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PDBsum entry 2a11
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Transcription,translation,hydrolase
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PDB id
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2a11
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References listed in PDB file
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Key reference
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Title
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Structure of the nuclease domain of ribonuclease III from m. Tuberculosis at 2.1 a.
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Authors
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D.L.Akey,
J.M.Berger.
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Ref.
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Protein Sci, 2005,
14,
2744-2750.
[DOI no: ]
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PubMed id
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Abstract
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RNase III enzymes are a highly conserved family of proteins that specifically
cleave double-stranded (ds)RNA. These proteins are involved in a diverse group
of functions, including ribosomal RNA processing, mRNA maturation and decay,
snRNA and snoRNA processing, and RNA interference. Here we report the crystal
structure of the nuclease domain of RNase III from the pathogen Mycobacterium
tuberculosis. Although globally similar to other RNase III folds, this structure
has some features not observed in previously reported models. These include the
presence of an additional metal ion near the catalytic site, as well as
conserved secondary structural elements that are proposed to have functional
roles in the recognition of dsRNAs.
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Figure 2.
Figure 2. (A) Stereo diagram of dimer interface showing the
surface of one monomer and the interacting region from the
adjacent monomer. The surface regions corresponding to the polar
side-chain atoms which bridge the interface are colored: Glu68
OE1 and OE2, red; Tyr130 OH, red; and Arg42 NH1 and NH2, blue.
The box outlines the region shown in B. (B) 2F[o]-F[c] refined
electron density map contoured at 1.5  detailing the
interaction between Arg42 and backbone carbonyls of residues
Phe60' through Ser67' of the dimermate. (C) A-form dsRNA modeled
on the TB nuclease domain so that the scissile phosphates (green
spheres) lie adjacent to the A-site metal ions (yellow spheres).
The 2°-site ions are shown in magenta. The bases forming the
two-nucleotide overhang product are indicated with orange bars.
This arrangement places the minor groove corresponding to the
distal box "anti-determinant" bases (cyan) (Zhang and Nicholson
1997) in close proximity to helices  2' and 5' (red).
Surface electrostatics calculation using APBS (D) (Baker et al.
2001) and surface conservation (E) (Glaser et al. 2003) show
negatively charged and conserved surface residues which align
with the proposed dsRNA binding region.
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The above figure is
reprinted
by permission from the Protein Society:
Protein Sci
(2005,
14,
2744-2750)
copyright 2005.
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