PDBsum entry 1k8a

Ribosome

PDB id: 1k8a

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

CAI

Metals

__K ×3

_NA ×83

_CL ×23

_MG ×119

_CD ×5

Waters ×7850

* Residue conservation analysis

References listed in PDB file

Key reference

Title

The structures of four macrolide antibiotics bound to the large ribosomal subunit.

Authors

J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz.

Ref.

Mol Cell, 2002, 10, 117-128. [DOI no: 10.1016/S1097-2765(02)00570-1]

PubMed id

12150912

Abstract

Crystal structures of the Haloarcula marismortui large ribosomal subunit complexed with the 16-membered macrolide antibiotics carbomycin A, spiramycin, and tylosin and a 15-membered macrolide, azithromycin, show that they bind in the polypeptide exit tunnel adjacent to the peptidyl transferase center. Their location suggests that they inhibit protein synthesis by blocking the egress of nascent polypeptides. The saccharide branch attached to C5 of the lactone rings extends toward the peptidyl transferase center, and the isobutyrate extension of the carbomycin A disaccharide overlaps the A-site. Unexpectedly, a reversible covalent bond forms between the ethylaldehyde substituent at the C6 position of the 16-membered macrolides and the N6 of A2103 (A2062, E. coli). Mutations in 23S rRNA that result in clinical resistance render the binding site less complementary to macrolides.

Figure 1.
Figure 1. Chemical Structures of the Macrolides, Tylosin, Carbomycin A, Spiramycin, Azithromycin, and ErythromycinAtoms in these figures and in the Protein Data Bank coordinate files (1K8A, 1K9M, 1M1K, and 1KD1) are named according to Paesen et al. (1995), with the numbering of the atoms of the lactone ring starting at the ester bond. Oxygen atoms are numbered according to the adjacent carbon atoms, and sugar atom numbers are modified by suffixes A, B, or C to distinguish mycaminose, mycarose, and any additional sugar, respectively.

Figure 5.
Figure 5. Comparison of the Interactions of Different Macrolides with the Ribosome(A) Carbomycin (red), tylosin (orange), spiramycin (yellow), and azithromycin (blue) bind the ribosome in an almost identical fashion and cover G2099 (A2058) and A2100 (2059) (green spheres). The lactone ring is extended further into the tunnel by mycinose on tylosin and forosamine on spiramycin. The disaccharide moiety extends the 16-membered macrolides in the opposite direction toward the catalytic center. Upon 16-membered macrolide binding (but not azithromycin), the base of A2103 (2062) (dark green) moves (curved white line) from its location against the wall of the exit tunnel to an extended conformation (light green sticks) and forms a covalent bond with the macrolide (orange sticks). The isobutyrate group of carbomycin A (red) reaches into the tRNA A-site (dark blue and purple spheres). The mycinose moiety of tylosin (orange) contacts protein L22. The forosamine moiety of spiramycin (yellow) contacts L4. The cladinose sugar of azithromycin binds in a fourth sugar binding pocket. These three macrolides were aligned by least squares superimposition of the phosphates of ribosomal RNA.(B) Alignment of erythromycin (white) bound to the D. radiodurans large subunit (Schlünzen et al., 2001) with azithromycin (blue) bound to the H. marismortui large subunit.

The above figures are reprinted by permission from Cell Press: Mol Cell (2002, 10, 117-128) copyright 2002.

Secondary reference #1

Title

The complete atomic structure of the large ribosomal subunit at 2.4 a resolution.

Authors

N.Ban, P.Nissen, J.Hansen, P.B.Moore, T.A.Steitz.

Ref.

Science, 2000, 289, 905-920. [DOI no: 10.1126/science.289.5481.905]

PubMed id

10937989

Figure 1.
Fig. 1. Portions of the experimental 2.4 Å resolution electron density map. (A) A stereo view of a junction between 23S rRNA domains II, III, IV, and V having a complex structure that is clearly interpretable. The electron density is contoured at 2 . The bases are white and the backbones are colored by domain as specified in Fig. 4. (B) The extended region of L3 interacting with its surrounding RNA, where the red RNA density is contoured at 2 and the blue protein density is contoured at 1.5 . (C) Detail in the L2 region showing a bound Mg2+ ion. (D) Detail from L2 showing amino acid side chains. (E) Helices 94 through 97 from domain VI. The red contour level is at 2 , and the yellow contour at 6 shows the positions of the higher electron density phosphate groups.

Figure 2.
Fig. 2. The H. marismortui large ribosomal subunit in the rotated crown view. The L7/L12 stalk is to the right, the L1 stalk is to the left, and the central protuberance (CP) is at the top. In this view, the surface of the subunit that interacts with the small subunit faces the reader. RNA is shown in gray in a pseudo-space-filling rendering. The backbones of the proteins visible are rendered in gold. The Yarus inhibitor bound to the peptidyl transferase site of the subunit is indicated in green (64). The particle is approximately 250 Å across.

The above figures are reproduced from the cited reference with permission from the AAAs

Secondary reference #2

Title

The structural basis of ribosome activity in peptide bond synthesis.

Authors

P.Nissen, J.Hansen, N.Ban, P.B.Moore, T.A.Steitz.

Ref.

Science, 2000, 289, 920-930. [DOI no: 10.1126/science.289.5481.920]

PubMed id

10937990

Figure 1.
Fig. 1. Chemical structures of ribosome peptidyl transferase substrates and analogs. (A) The tetrahedral carbon intermediate produced during peptide bond formation; the tetrahedral carbon is indicated by an arrow. (B) The transition state analog formed by coupling the 3' OH of CCdA to the amino group of the O-methyl tyrosine residue of puromycin via a phosphate group, CCdA-p-Puro (a gift from Michael Yarus) (32). (C) An N-amino-acylated mini-helix constructed to target the A-site. The oligonucleotide sequence 5'-CCGGCGGGCUGGUUCAAACCGGCCCGCCGGA- CC-3' puromycin should form 13 base pairs. The construct is based on a mini-helix known to be a suitable substrate for amino-acylation by Tyr-tRNA synthetase. The 3' OH of its terminal C is coupled to the 5' OH of the N6-dimethyl A moiety of puromycin by a phosphodiester bond.

Figure 7.
Fig. 7. Conserved nucleotides in the peptidyl transferase region with bound CCdA-p-Puro. A space-filling representation of the active site region with the Yarus inhibitor viewed down the active site cleft. All atoms belonging to 23S rRNA nucleotides that are >95% conserved in all three kingdoms (44) are colored red and all other nucleotides are white; the inhibitor is colored blue.

The above figures are reproduced from the cited reference with permission from the AAAs