3M7N
archaeoglobus fulgidus exosome with RNA bound to the active site
Summary for 3M7N
Entry DOI | 10.2210/pdb3m7n/pdb |
Related | 2BA0 2BA1 3M85 |
Descriptor | Putative uncharacterized protein AF_0206, Probable exosome complex exonuclease 1, Probable exosome complex exonuclease 2, ... (6 entities in total) |
Functional Keywords | exosome, rna, exonuclease, hydrolase, nuclease, hydrolase-rna complex, hydrolase/rna |
Biological source | Archaeoglobus fulgidus More |
Cellular location | Cytoplasm (Potential): O29757 O29756 |
Total number of polymer chains | 12 |
Total formula weight | 237048.01 |
Authors | Hartung, S.,Hopfner, K.-P. (deposition date: 2010-03-16, release date: 2010-04-28, Last modification date: 2023-11-01) |
Primary citation | Hartung, S.,Niederberger, T.,Hartung, M.,Tresch, A.,Hopfner, K.-P. Quantitative analysis of processive RNA degradation by the archaeal RNA exosome Nucleic Acids Res., 38:5166-5176, 2010 Cited by PubMed Abstract: RNA exosomes are large multisubunit assemblies involved in controlled RNA processing. The archaeal exosome possesses a heterohexameric processing chamber with three RNase-PH-like active sites, capped by Rrp4- or Csl4-type subunits containing RNA-binding domains. RNA degradation by RNA exosomes has not been studied in a quantitative manner because of the complex kinetics involved, and exosome features contributing to efficient RNA degradation remain unclear. Here we derive a quantitative kinetic model for degradation of a model substrate by the archaeal exosome. Markov Chain Monte Carlo methods for parameter estimation allow for the comparison of reaction kinetics between different exosome variants and substrates. We show that long substrates are degraded in a processive and short RNA in a more distributive manner and that the cap proteins influence degradation speed. Our results, supported by small angle X-ray scattering, suggest that the Rrp4-type cap efficiently recruits RNA but prevents fast RNA degradation of longer RNAs by molecular friction, likely by RNA contacts to its unique KH-domain. We also show that formation of the RNase-PH like ring with entrapped RNA is not required for high catalytic efficiency, suggesting that the exosome chamber evolved for controlled processivity, rather than for catalytic chemistry in RNA decay. PubMed: 20392821DOI: 10.1093/nar/gkq238 PDB entries with the same primary citation |
Experimental method | X-RAY DIFFRACTION (2.4 Å) |
Structure validation
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