Endoribonuclease III is a class 1 RNase III hydrolase enzyme. In general its function, which seems to be universally conserved, is the binding to and cleavage of dsRNA. Endoribonuclease III appears to be crucial for an organisms ability to rapidly adapt to environmental changes through dsRNA processing and decay.
Universally, it has been shown to mediate RNA turnover at the post-transcriptional level through processing rRNAs, tRNAs, some mRNAs, as well as non-coding dsRNAs. In microbes, RNase III has been shown that it also represses the synthesis of virulence factors (through the cleavage of foreign RNA.) [1]
In eukaryotes, RNase III has also been shown to generate microRNAs and siRNAs, which are central to gene regulation pathways.
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Example page for Green fluorescent protein ("GFP")
RNase III (1O0W)
(GFP),originally isolated from the jellyfish Aequorea victoria (PDB entry 1ema), fluorsceses green (509nm) when exposed to blue light (395nm and 475nm). It is one of the most important proteins used in biological research because it can be used to tag otherwise invisible gene products of interest and thus observe their existence, location and movement.
Exploring the Structure
Structure
The monomer of Aquifex aeolicus RNase III (Aa-RNase III) are composed of an endonuclease domain (endoND) and a dsRNA binding domain (dsRBD)[1]. The sequence of the endoND is characterized by a stretch of conserved residues (37ERLEFLGD44 in Aa-RNase III), which is known as the RNase III signature motif and makes up a large part of the active center. RNase III can affect gene expression in either of two ways: as a processing enzyme which RNase III cleaves both natural and synthetic dsRNA into small duplex products averaging 10–18 base pairs in length, or as a binding protein which binds and stabilizes certain RNAs, thus suppressing the expression of certain genes[2, 3].
On the basis of the structural and biochemical data, catalytic models were proposed before the structure of a catalytic complex became available. The crystal structure shows that Aa-RNase III is composed of a symmetric dimer. In addition, in vivo data suggested that E110, E37, D44, and E64 are essential for catalysis[4]. This led to the model of the proteins active centers, which can accommodate a dsRNA substrate, each containing two different RNA cleavage sites, D44/E110 and E37/E64. Specifically, E64 from each partner subunit, along with E37, E40, and D44 are located in the signature motif located at each end of a valley-like cleft[5]. Comparing the structure of Aa-RNase III with the structure of RNA-free Thermotoga maritima RNase III (RNA-free Tm-RNase III, PDB ID code 1O0W)[6] shows that there is dramatic rotation and shift of dsRBD due to RNA binding.
Structural highlights
Function
Disease
Relevance
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