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3M7N

archaeoglobus fulgidus exosome with RNA bound to the active site

Summary for 3M7N
Entry DOI10.2210/pdb3m7n/pdb
Related2BA0 2BA1 3M85
DescriptorPutative uncharacterized protein AF_0206, Probable exosome complex exonuclease 1, Probable exosome complex exonuclease 2, ... (6 entities in total)
Functional Keywordsexosome, rna, exonuclease, hydrolase, nuclease, hydrolase-rna complex, hydrolase/rna
Biological sourceArchaeoglobus fulgidus
More
Cellular locationCytoplasm (Potential): O29757 O29756
Total number of polymer chains12
Total formula weight237048.01
Authors
Hartung, S.,Hopfner, K.-P. (deposition date: 2010-03-16, release date: 2010-04-28, Last modification date: 2023-11-01)
Primary citationHartung, 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: 20392821
DOI: 10.1093/nar/gkq238
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.4 Å)
Structure validation

237735

数据于2025-06-18公开中

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