1FFZ

LARGE RIBOSOMAL SUBUNIT COMPLEXED WITH R(CC)-DA-PUROMYCIN

Summary for 1FFZ

• Entry DOI: 10.2210/pdb1ffz/pdb
• Related: 1FFK 1FG0
• Descriptor: 23S RIBOSOMAL RNA, R(P*CP*C*)-D(P*A)-R(P*(PU)) (2 entities in total)
• Functional Keywords: ribosome assembly, rna-rna complex, ribozyme, ribosomal rna, ribosome
• Biological source: Haloarcula marismortui
• Total number of polymer chains: 2
• Total formula weight: 196263.77

Authors

Nissen, P.,Hansen, J.,Ban, N.,Moore, P.B.,Steitz, T.A. (deposition date: 2000-07-26, release date: 2000-08-28, Last modification date: 2024-02-07)

Primary citation

Nissen, P.,Hansen, J.,Ban, N.,Moore, P.B.,Steitz, T.A.
The structural basis of ribosome activity in peptide bond synthesis.
Science, 289:920-930, 2000

PubMed Abstract: Using the atomic structures of the large ribosomal subunit from Haloarcula marismortui and its complexes with two substrate analogs, we establish that the ribosome is a ribozyme and address the catalytic properties of its all-RNA active site. Both substrate analogs are contacted exclusively by conserved ribosomal RNA (rRNA) residues from domain V of 23S rRNA; there are no protein side-chain atoms closer than about 18 angstroms to the peptide bond being synthesized. The mechanism of peptide bond synthesis appears to resemble the reverse of the acylation step in serine proteases, with the base of A2486 (A2451 in Escherichia coli) playing the same general base role as histidine-57 in chymotrypsin. The unusual pK(a) (where K(a) is the acid dissociation constant) required for A2486 to perform this function may derive in part from its hydrogen bonding to G2482 (G2447 in E. coli), which also interacts with a buried phosphate that could stabilize unusual tautomers of these two bases. The polypeptide exit tunnel is largely formed by RNA but has significant contributions from proteins L4, L22, and L39e, and its exit is encircled by proteins L19, L22, L23, L24, L29, and L31e.

PubMed: 10937990
DOI: 10.1126/science.289.5481.920

Experimental method

X-RAY DIFFRACTION (3.2 Å)