4BA1
Archaeal exosome (Rrp4-Rrp41(D182A)-Rrp42) bound to inorganic phosphate
Summary for 4BA1
| Entry DOI | 10.2210/pdb4ba1/pdb |
| Related | 2BR2 2C37 2C38 2C39 2JE6 2JEA 2JEB 4BA2 |
| Descriptor | PROBABLE EXOSOME COMPLEX EXONUCLEASE 2, PROBABLE EXOSOME COMPLEX EXONUCLEASE 1, PROBABLE EXOSOME COMPLEX RNA-BINDING PROTEIN 1, ... (8 entities in total) |
| Functional Keywords | hydrolase, rna degradation |
| Biological source | SULFOLOBUS SOLFATARICUS More |
| Cellular location | Cytoplasm (Potential): Q9UXC0 Q9UXC2 Q9UXC4 |
| Total number of polymer chains | 3 |
| Total formula weight | 86969.60 |
| Authors | Lorentzen, E.,Conti, E. (deposition date: 2012-09-10, release date: 2012-10-03, Last modification date: 2023-12-20) |
| Primary citation | Lorentzen, E.,Conti, E. Crystal Structure of a 9-Subunit Archaeal Exosome in Pre-Catalytic States of the Phosphorolytic Reaction. Archaea, 2012:21869-, 2012 Cited by PubMed Abstract: The RNA exosome is an important protein complex that functions in the 3' processing and degradation of RNA in archaeal and eukaryotic organisms. The archaeal exosome is functionally similar to bacterial polynucleotide phosphorylase (PNPase) and RNase PH enzymes as it uses inorganic phosphate (Pi) to processively cleave RNA substrates releasing nucleoside diphosphates. To shed light on the mechanism of catalysis, we have determined the crystal structures of mutant archaeal exosome in complex with either Pi or with both RNA and Pi at resolutions of 1.8 Å and 2.5 Å, respectively. These structures represent views of precatalytic states of the enzyme and allow the accurate determination of the substrate binding geometries. In the structure with both Pi and RNA bound, the Pi closely approaches the phosphate of the 3'-end nucleotide of the RNA and is in a perfect position to perform a nucleophilic attack. The presence of negative charge resulting from the close contacts between the phosphates appears to be neutralized by conserved positively charged residues in the active site of the archaeal exosome. The high degree of structural conservation between the archaeal exosome and the PNPase including the requirement for divalent metal ions for catalysis is discussed. PubMed: 23319881DOI: 10.1155/2012/721869 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.8 Å) |
Structure validation
Download full validation report
