1YT3

Crystal Structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing

Summary for 1YT3

• Entry DOI: 10.2210/pdb1yt3/pdb
• Descriptor: Ribonuclease D, SULFATE ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: rnase; exoribonuclease; ribonuclease; exonuclease; nuclease; hydrolase; trna processing, hydrolase, translation
• Biological source: Escherichia coli
• Cellular location: Cytoplasm: P09155
• Total number of polymer chains: 1
• Total formula weight: 43778.61

Authors

Zuo, Y.,Wang, Y.,Malhotra, A. (deposition date: 2005-02-09, release date: 2005-08-09, Last modification date: 2024-04-03)

Primary citation

Zuo, Y.,Wang, Y.,Malhotra, A.
Crystal Structure of Escherichia coli RNase D, an Exoribonuclease Involved in Structured RNA Processing
Structure, 13:973-984, 2005

PubMed Abstract: RNase D (RND) is one of seven exoribonucleases identified in Escherichia coli. RNase D has homologs in many eubacteria and eukaryotes, and has been shown to contribute to the 3' maturation of several stable RNAs. Here, we report the 1.6 A resolution crystal structure of E. coli RNase D. The conserved DEDD residues of RNase D fold into an arrangement very similar to the Klenow fragment exonuclease domain. Besides the catalytic domain, RNase D also contains two structurally similar alpha-helical domains with no discernible sequence homology between them. These closely resemble the HRDC domain previously seen in RecQ-family helicases and several other proteins acting on nucleic acids. More interestingly, the DEDD catalytic domain and the two helical domains come together to form a ring-shaped structure. The ring-shaped architecture of E. coli RNase D and the HRDC domains likely play a major role in determining the substrate specificity of this exoribonuclease.

PubMed: 16004870
DOI: 10.1016/j.str.2005.04.015

Experimental method

X-RAY DIFFRACTION (1.6 Å)