Crystal structure of Escherichia coli RNase D, an exoribonuclease involved in structured RNA processing.
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.
Zuo
Yuhong
Y
Department of Biochemistry and Molecular Biology, University of Miami School of Medicine, PO Box 016129, Miami, FL 33101, USA.
Wang
Yong
Y
Malhotra
Arun
A
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D020134:Catalytic Domain; D002845:Chromatography; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004722:Endoribonucleases / Q000737:chemistry; D004926:Escherichia coli / Q000201:enzymology* / Q000378:metabolism; D029968:Escherichia coli Proteins / Q000737:chemistry; D006860:Hydrogen Bonding; D007477:Ions; D008958:Models, Molecular; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry; D012313:RNA / Q000737:chemistry; D012329:RNA, Bacterial; D043244:Ribonuclease III / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
D029968:Escherichia coli Proteins; D007477:Ions; D011506:Proteins; D012329:RNA, Bacterial; D012313:RNA; D004722:Endoribonucleases; D043244:Ribonuclease III