2JA9

Structure of the N-terminal deletion of yeast exosome component Rrp40

Summary for 2JA9

• Entry DOI: 10.2210/pdb2ja9/pdb
• Descriptor: EXOSOME COMPLEX EXONUCLEASE RRP40 (2 entities in total)
• Functional Keywords: rna-binding protein, rna, exosome, nuclease, s1 domain, kh domain, hydrolase, rna-binding, exonuclease, nuclear protein, rrna processing, nucleic-acid binding, rna binding protein
• Biological source: SACCHAROMYCES CEREVISIAE (BAKERS' YEAST)
• Cellular location: Cytoplasm: Q08285
• Total number of polymer chains: 1
• Total formula weight: 19607.51

Authors

Oddone, A.,Lorentzen, E.,Basquin, J.,Gasch, A.,Rybin, V.,Conti, E.,Sattler, M. (deposition date: 2006-11-24, release date: 2006-12-13, Last modification date: 2024-05-08)

Primary citation

Oddone, A.,Lorentzen, E.,Basquin, J.,Gasch, A.,Rybin, V.,Conti, E.,Sattler, M.
Structural and Biochemical Characterization of the Yeast Exosome Component Rrp40
Embo Rep., 8:63-, 2007

PubMed Abstract: The exosome is a protein complex that is important in both degradation and 3'-processing of eukaryotic RNAs. We present the crystal structure of the Rrp40 exosome subunit from Saccharomyces cerevisiae at a resolution of 2.2 A. The structure comprises an S1 domain and an unusual KH (K homology) domain. Close packing of the S1 and KH domains is stabilized by a GxNG sequence, which is uniquely conserved in exosome KH domains. Nuclear magnetic resonance data reveal the presence of a manganese-binding site at the interface of the two domains. Isothermal titration calorimetry shows that Rrp40 and archaeal Rrp4 alone have very low intrinsic affinity for RNA. The affinity of an archaeal core exosome for RNA is significantly increased in the presence of the S1-KH subunit Rrp4, indicating that multiple subunits might contribute to cooperative binding of RNA substrates by the exosome.

PubMed: 17159918
DOI: 10.1038/SJ.EMBOR.7400856

Experimental method

X-RAY DIFFRACTION (2.2 Å)