PDBsum entry 1q81

Ribosome

PDB id: 1q81

Contents

Protein chains

237 a.a. *

337 a.a. *

246 a.a. *

140 a.a. *

172 a.a. *

119 a.a. *

29 a.a. *

156 a.a. *

142 a.a. *

132 a.a. *

145 a.a. *

194 a.a. *

186 a.a. *

115 a.a. *

143 a.a. *

95 a.a. *

150 a.a. *

81 a.a. *

119 a.a. *

53 a.a. *

65 a.a. *

154 a.a. *

82 a.a. *

142 a.a. *

73 a.a. *

56 a.a. *

46 a.a. *

92 a.a. *

DNA/RNA

Ligands

_DC-_DC

PPU

Metals

_CL ×22

_NA ×86

_MG ×117

_CD ×5

__K ×2

Waters ×7869

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural insights into peptide bond formation.

Authors

J.L.Hansen, T.M.Schmeing, P.B.Moore, T.A.Steitz.

Ref.

Proc Natl Acad Sci U S A, 2002, 99, 11670-11675. [DOI no: 10.1073/pnas.172404099]

PubMed id

12185246

Abstract

The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.

Figure 1.
Fig. 1. Chemical structures of peptidyl transferase substrate analogues. (A) CCA-pcb is active as a P site substrate and binds to only the P site in the presence of the antibiotic, sparsomycin. (B) An aminoacylated RNA minihelix binds to the A site. (C) CCdA-phosphate-puromycin is an intermediate analogue containing A and P site-binding components. (D) CC-puromycin-phenylalanine-caproic acid-biotin and deacylated CCA are products of the peptidyl transferase reaction.

Figure 2.
Fig. 2. Experimental electron density maps. (A) An F[o] F[o] electron density map (blue net) contoured at 4.0 shows density corresponding to CCA-pcb (green) in the P site and sparsomycin (yellow). Additional density corresponds to altered conformations of nucleotides such as A2637 (orange). (B) F[o] F[o] electron density map of CCA-pcb shows that in the absence of sparsomycin, the P site substrate is bound equally between the P site (green) and the A site (red).