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PDBsum entry 1nji
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
1nji

 

 

 

 

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JSmol PyMol  
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
CLM
Metals
_NA ×85
_CL ×22
_MG ×117
_CD ×5
__K ×2
Waters ×7867
* Residue conservation analysis
PDB id:
1nji
Name: Ribosome
Title: Structure of chloramphenicol bound to the 50s ribosomal subunit
Structure: 23s ribosomal RNA. Chain: a. 5s ribosomal RNA. Chain: b. 50s ribosomal protein l2p. Chain: c. Synonym: hmal2, hl4. 50s ribosomal protein l3p. Chain: d.
Source: Haloarcula marismortui. Organism_taxid: 2238. Other_details: cultured cells. Other_details: cultured cells
Biol. unit: 30mer (from PQS)
Resolution:
3.00Å     R-factor:   0.176     R-free:   0.209
Authors: J.L.Hansen,P.B.Moore,T.A.Steitz
Key ref:
J.L.Hansen et al. (2003). Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit. J Mol Biol, 330, 1061-1075. PubMed id: 12860128 DOI: 10.1016/S0022-2836(03)00668-5
Date:
31-Dec-02     Release date:   22-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P20276  (RL2_HALMA) -  Large ribosomal subunit protein uL2 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		240 a.a.
237 a.a.*
Protein chain
Pfam   ArchSchema ?
P20279  (RL3_HALMA) -  Large ribosomal subunit protein uL3 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		338 a.a.
337 a.a.
Protein chain
Pfam   ArchSchema ?
P12735  (RL4_HALMA) -  Large ribosomal subunit protein uL4 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		246 a.a.
246 a.a.*
Protein chain
Pfam   ArchSchema ?
P14124  (RL5_HALMA) -  Large ribosomal subunit protein uL5 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		177 a.a.
140 a.a.
Protein chain
Pfam   ArchSchema ?
P14135  (RL6_HALMA) -  Large ribosomal subunit protein uL6 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		178 a.a.
172 a.a.
Protein chain
Pfam   ArchSchema ?
P12743  (RL7A_HALMA) -  Large ribosomal subunit protein eL8 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		120 a.a.
119 a.a.*
Protein chain
Pfam   ArchSchema ?
P15825  (RL10_HALMA) -  Large ribosomal subunit protein uL10 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		348 a.a.
29 a.a.*
Protein chain
Pfam   ArchSchema ?
P60617  (RL10E_HALMA) -  Large ribosomal subunit protein uL16 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		177 a.a.
156 a.a.*
Protein chain
Pfam   ArchSchema ?
P29198  (RL13_HALMA) -  Large ribosomal subunit protein uL13 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		145 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P22450  (RL14_HALMA) -  Large ribosomal subunit protein uL14 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		132 a.a.
132 a.a.
Protein chain
Pfam   ArchSchema ?
P12737  (RL15_HALMA) -  Large ribosomal subunit protein uL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		165 a.a.
145 a.a.
Protein chain
Pfam   ArchSchema ?
P60618  (RL15E_HALMA) -  Large ribosomal subunit protein eL15 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		196 a.a.
194 a.a.*
Protein chain
Pfam   ArchSchema ?
P14123  (RL18_HALMA) -  Large ribosomal subunit protein uL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		187 a.a.
186 a.a.
Protein chain
Pfam   ArchSchema ?
P12733  (RL18E_HALMA) -  Large ribosomal subunit protein eL18 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		116 a.a.
115 a.a.
Protein chain
Pfam   ArchSchema ?
P14119  (RL19E_HALMA) -  Large ribosomal subunit protein eL19 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		149 a.a.
143 a.a.*
Protein chain
Pfam   ArchSchema ?
P12734  (RL21_HALMA) -  Large ribosomal subunit protein eL21 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		96 a.a.
95 a.a.
Protein chain
Pfam   ArchSchema ?
P10970  (RL22_HALMA) -  Large ribosomal subunit protein uL22 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		155 a.a.
150 a.a.
Protein chain
Pfam   ArchSchema ?
P12732  (RL23_HALMA) -  Large ribosomal subunit protein uL23 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		85 a.a.
81 a.a.
Protein chain
Pfam   ArchSchema ?
P10972  (RL24_HALMA) -  Large ribosomal subunit protein uL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		120 a.a.
119 a.a.
Protein chain
Pfam   ArchSchema ?
P14116  (RL24E_HALMA) -  Large ribosomal subunit protein eL24 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		67 a.a.
53 a.a.
Protein chain
Pfam   ArchSchema ?
P10971  (RL29_HALMA) -  Large ribosomal subunit protein uL29 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		71 a.a.
65 a.a.
Protein chain
Pfam   ArchSchema ?
P14121  (RL30_HALMA) -  Large ribosomal subunit protein uL30 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		154 a.a.
154 a.a.
Protein chain
Pfam   ArchSchema ?
P18138  (RL31_HALMA) -  Large ribosomal subunit protein eL31 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
82 a.a.
Protein chain
Pfam   ArchSchema ?
P12736  (RL32_HALMA) -  Large ribosomal subunit protein eL32 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		241 a.a.
142 a.a.
Protein chain
Pfam   ArchSchema ?
P60619  (RL37A_HALMA) -  Large ribosomal subunit protein eL43 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
73 a.a.*
Protein chain
Pfam   ArchSchema ?
P32410  (RL37_HALMA) -  Large ribosomal subunit protein eL37 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		57 a.a.
56 a.a.
Protein chain
Pfam   ArchSchema ?
P22452  (RL39_HALMA) -  Large ribosomal subunit protein eL39 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		50 a.a.
46 a.a.*
Protein chain
Pfam   ArchSchema ?
P32411  (RL44E_HALMA) -  Large ribosomal subunit protein eL42 from Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)
Seq:
Struc: 		92 a.a.
92 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 185 residue positions (black crosses)

DNA/RNA chains
  U-A-U-G-C-C-A-G-C-U-G-G-U-G-G-A-U-U-G-C-U-C-G-G-C-U-C-A-G-G-C-G-C-U-G-A-U-G-A- ... 2754 bases
  U-U-A-G-G-C-G-G-C-C-A-C-A-G-C-G-G-U-G-G-G-G-U-U-G-C-C-U-C-C-C-G-U-A-C-C-C-A-U- 122 bases

 Enzyme reactions 
   Enzyme class: Chains C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z, 1, 2, 3, 4: E.C.?
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1016/S0022-2836(03)00668-5 J Mol Biol 330:1061-1075 (2003)
PubMed id: 12860128  
 
 
Structures of five antibiotics bound at the peptidyl transferase center of the large ribosomal subunit.
J.L.Hansen, P.B.Moore, T.A.Steitz.
 
  ABSTRACT  
 
Structures of anisomycin, chloramphenicol, sparsomycin, blasticidin S, and virginiamycin M bound to the large ribosomal subunit of Haloarcula marismortui have been determined at 3.0A resolution. Most of these antibiotics bind to sites that overlap those of either peptidyl-tRNA or aminoacyl-tRNA, consistent with their functioning as competitive inhibitors of peptide bond formation. Two hydrophobic crevices, one at the peptidyl transferase center and the other at the entrance to the peptide exit tunnel play roles in binding these antibiotics. Midway between these crevices, nucleotide A2103 of H.marismortui (2062 Escherichia coli) varies in its conformation and thereby contacts antibiotics bound at either crevice. The aromatic ring of anisomycin binds to the active-site hydrophobic crevice, as does the aromatic ring of puromycin, while the aromatic ring of chloramphenicol binds to the exit tunnel hydrophobic crevice. Sparsomycin contacts primarily a P-site bound substrate, but also extends into the active-site hydrophobic crevice. Virginiamycin M occupies portions of both the A and P-site, and induces a conformational change in the ribosome. Blasticidin S base-pairs with the P-loop and thereby mimics C74 and C75 of a P-site bound tRNA.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Electron density maps. Unbiased F[o] -F[c] difference Fourier maps (gray netting) contoured at 3.0s reveal the location, orientation, and conformation of these antibiotics. (a), (b) Nucleotides of ribosomal RNA (gray sticks) that are either protected or deprotected by the anisomycin (a) or chloramphenicol (b) from chemical modification (green) or that upon mutation confer resistance to the given antibiotic (orange) are provided for context. (c) The placement and conformation of virginiamycin M (blue) in the corresponding doughnut shaped electron density is unambiguous. (d) Blasticidin S (purple) binds at two sites, but density for the second site is weaker and incomplete. (e) Sparsomycin (green) binds only in the presence of a P-site bound substrate (orange). A2637 (2602) (gray stick) is apparent in the difference map because it changes conformation upon substrate binding. 		Figure 7.
Figure 7. Sparsomycin binding site. Sparsomycin (green) is sandwiched between the CCA end of P-site bound substrate analogue, CCA-phe-cap-biotin (large spheres) and the base of A2637 (2602) (gray sticks). Hydrogen bonds and ionic interactions are shown as dotted lines. A magnesium ion is purple and water molecules are small red spheres. The sulfur (yellow) containing tail of sparsomycin enters the active-site hydrophobic crevice between A2486 (2451) (gray sticks) and C2487 (2452) (orange sticks, resistance mutation).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 1061-1075) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21513713 A.Fabbretti, C.O.Gualerzi, and L.Brandi (2011).
How to cope with the quest for new antibiotics.
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21356104 R.E.Valas, and P.E.Bourne (2011).
The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon.
  Biol Direct, 6, 16.  
20494981 H.David-Eden, A.S.Mankin, and Y.Mandel-Gutfreund (2010).
Structural signatures of antibiotic binding sites on the ribosome.
  Nucleic Acids Res, 38, 5982-5994.  
20876128 J.A.Dunkle, L.Xiong, A.S.Mankin, and J.H.Cate (2010).
Structures of the Escherichia coli ribosome with antibiotics bound near the peptidyl transferase center explain spectra of drug action.
  Proc Natl Acad Sci U S A, 107, 17152-17157.
PDB codes: 3oaq 3oar 3oas 3oat 3ofa 3ofb 3ofc 3ofd 3ofo 3ofp 3ofq 3ofr 3ofx 3ofy 3ofz 3og0
20464003 J.Piel (2010).
Biosynthesis of polyketides by trans-AT polyketide synthases.
  Nat Prod Rep, 27, 996.  
20705654 M.H.Rhodin, and J.D.Dinman (2010).
A flexible loop in yeast ribosomal protein L11 coordinates P-site tRNA binding.
  Nucleic Acids Res, 38, 8377-8389.  
20822442 M.Morar, and G.D.Wright (2010).
The genomic enzymology of antibiotic resistance.
  Annu Rev Genet, 44, 25-51.  
20080686 T.Auerbach, I.Mermershtain, C.Davidovich, A.Bashan, M.Belousoff, I.Wekselman, E.Zimmerman, L.Xiong, D.Klepacki, K.Arakawa, H.Kinashi, A.S.Mankin, and A.Yonath (2010).
The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics.
  Proc Natl Acad Sci U S A, 107, 1983-1988.
PDB code: 3jq4
20151411 X.Ge, and B.Roux (2010).
Calculation of the standard binding free energy of sparsomycin to the ribosomal peptidyl-transferase P-site using molecular dynamics simulations with restraining potentials.
  J Mol Recognit, 23, 128-141.  
19465765 D.M.Pettigrew, P.Roversi, S.G.Davies, A.J.Russell, and S.M.Lea (2009).
A structural study of the interaction between the Dr haemagglutinin DraE and derivatives of chloramphenicol.
  Acta Crystallogr D Biol Crystallogr, 65, 513-522.
PDB codes: 2jkj 2jkl 2jkn 2w5p
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
19019162 E.Diago-Navarro, L.Mora, R.H.Buckingham, R.Díaz-Orejas, and M.Lemonnier (2009).
Novel Escherichia coli RF1 mutants with decreased translation termination activity and increased sensitivity to the cytotoxic effect of the bacterial toxins Kid and RelE.
  Mol Microbiol, 71, 66-78.  
19089882 E.Zimmerman, and A.Yonath (2009).
Biological implications of the ribosome's stunning stereochemistry.
  Chembiochem, 10, 63-72.  
19362093 G.Gürel, G.Blaha, P.B.Moore, and T.A.Steitz (2009).
U2504 determines the species specificity of the A-site cleft antibiotics: the structures of tiamulin, homoharringtonine, and bruceantin bound to the ribosome.
  J Mol Biol, 389, 146-156.
PDB codes: 3g4s 3g6e 3g71
19738021 G.Gürel, G.Blaha, T.A.Steitz, and P.B.Moore (2009).
Structures of triacetyloleandomycin and mycalamide A bind to the large ribosomal subunit of Haloarcula marismortui.
  Antimicrob Agents Chemother, 53, 5010-5014.
PDB codes: 3i55 3i56
19170872 H.Ramu, A.Mankin, and N.Vazquez-Laslop (2009).
Programmed drug-dependent ribosome stalling.
  Mol Microbiol, 71, 811-824.  
20007368 J.E.McLaughlin, M.A.Bin-Umer, A.Tortora, N.Mendez, S.McCormick, and N.E.Tumer (2009).
A genome-wide screen in Saccharomyces cerevisiae reveals a critical role for the mitochondria in the toxicity of a trichothecene mycotoxin.
  Proc Natl Acad Sci U S A, 106, 21883-21888.  
19741022 M.de la Peña, D.Dufour, and J.Gallego (2009).
Three-way RNA junctions with remote tertiary contacts: a recurrent and highly versatile fold.
  RNA, 15, 1949-1964.  
19284290 R.Kodym, E.Kodym, and M.D.Story (2009).
Short double-stranded RNAs of specific sequence activate ribosomal TAK1-D and induce a global inhibition of translation.
  Biol Chem, 390, 453-462.  
  19173642 S.Shoji, S.E.Walker, and K.Fredrick (2009).
Ribosomal translocation: one step closer to the molecular mechanism.
  ACS Chem Biol, 4, 93.  
18263608 A.Meskauskas, J.R.Russ, and J.D.Dinman (2008).
Structure/function analysis of yeast ribosomal protein L2.
  Nucleic Acids Res, 36, 1826-1835.  
18824477 A.N.Petrov, A.Meskauskas, S.C.Roshwalb, and J.D.Dinman (2008).
Yeast ribosomal protein L10 helps coordinate tRNA movement through the large subunit.
  Nucleic Acids Res, 36, 6187-6198.  
18636557 A.Vourekas, V.Stamatopoulou, C.Toumpeki, M.Tsitlaidou, and D.Drainas (2008).
Insights into functional modulation of catalytic RNA activity.
  IUBMB Life, 60, 669-683.  
19098107 C.Davidovich, A.Bashan, and A.Yonath (2008).
Structural basis for cross-resistance to ribosomal PTC antibiotics.
  Proc Natl Acad Sci U S A, 105, 20665-20670.  
18060665 C.Foster, and W.S.Champney (2008).
Characterization of a 30S ribosomal subunit assembly intermediate found in Escherichia coli cells growing with neomycin or paromomycin.
  Arch Microbiol, 189, 441-449.  
18282091 D.L.Theobald, and D.S.Wuttke (2008).
Accurate structural correlations from maximum likelihood superpositions.
  PLoS Comput Biol, 4, e43.  
18757750 D.N.Wilson, F.Schluenzen, J.M.Harms, A.L.Starosta, S.R.Connell, and P.Fucini (2008).
The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning.
  Proc Natl Acad Sci U S A, 105, 13339-13344.
PDB code: 3dll
18824514 D.Rodriguez-Correa, and A.E.Dahlberg (2008).
Kinetic and thermodynamic studies of peptidyltransferase in ribosomes from the extreme thermophile Thermus thermophilus.
  RNA, 14, 2314-2318.  
18663023 E.Skripkin, T.S.McConnell, J.DeVito, L.Lawrence, J.A.Ippolito, E.M.Duffy, J.Sutcliffe, and F.Franceschi (2008).
R chi-01, a new family of oxazolidinones that overcome ribosome-based linezolid resistance.
  Antimicrob Agents Chemother, 52, 3550-3557.  
18455733 G.Blaha, G.Gürel, S.J.Schroeder, P.B.Moore, and T.A.Steitz (2008).
Mutations outside the anisomycin-binding site can make ribosomes drug-resistant.
  J Mol Biol, 379, 505-519.
PDB codes: 3cc2 3cc4 3cc7 3cce 3ccj 3ccl 3ccm 3ccq 3ccr 3ccs 3ccu 3ccv 3cd6
18936244 H.Ishida, and S.Hayward (2008).
Path of nascent polypeptide in exit tunnel revealed by molecular dynamics simulation of ribosome.
  Biophys J, 95, 5962-5973.  
18256246 J.Esguerra, J.Warringer, and A.Blomberg (2008).
Functional importance of individual rRNA 2'-O-ribose methylations revealed by high-resolution phenotyping.
  RNA, 14, 649-656.  
18299405 L.K.Smith, and A.S.Mankin (2008).
Transcriptional and translational control of the mlr operon, which confers resistance to seven classes of protein synthesis inhibitors.
  Antimicrob Agents Chemother, 52, 1703-1712.  
18568365 M.C.Frigieri, M.V.João Luiz, L.H.Apponi, C.F.Zanelli, and S.R.Valentini (2008).
Synthetic lethality between eIF5A and Ypt1 reveals a connection between translation and the secretory pathway in yeast.
  Mol Genet Genomics, 280, 211-221.  
18205815 R.Elevi Bardavid, and A.Oren (2008).
Sensitivity of Haloquadratum and Salinibacter to antibiotics and other inhibitors: implications for the assessment of the contribution of Archaea and Bacteria to heterotrophic activities in hypersaline environments.
  FEMS Microbiol Ecol, 63, 309-315.  
18203742 R.Rakauskaite, and J.D.Dinman (2008).
rRNA mutants in the yeast peptidyltransferase center reveal allosteric information networks and mechanisms of drug resistance.
  Nucleic Acids Res, 36, 1497-1507.  
18382121 T.A.Steitz (2008).
Structural insights into the functions of the large ribosomal subunit, a major antibiotic target.
  Keio J Med, 57, 1.  
17401565 X.Wang, G.Kapral, L.Murray, D.Richardson, J.Richardson, and J.Snoeyink (2008).
RNABC: forward kinematics to reduce all-atom steric clashes in RNA backbone.
  J Math Biol, 56, 253-278.  
17386264 A.Meskauskas, and J.D.Dinman (2007).
Ribosomal protein L3: gatekeeper to the A site.
  Mol Cell, 25, 877-888.  
17591769 A.Yassin, and A.S.Mankin (2007).
Potential new antibiotic sites in the ribosome revealed by deleterious mutations in RNA of the large ribosomal subunit.
  J Biol Chem, 282, 24329-24342.  
17557852 C.I.Montero, M.R.Johnson, C.J.Chou, S.B.Conners, S.G.Geouge, S.Tachdjian, J.D.Nichols, and R.M.Kelly (2007).
Responses of wild-type and resistant strains of the hyperthermophilic bacterium Thermotoga maritima to chloramphenicol challenge.
  Appl Environ Microbiol, 73, 5058-5065.  
17146803 C.Shammas, J.A.Donarski, and V.Ramesh (2007).
NMR structure of the peptidyl transferase RNA inhibitor antibiotic amicetin.
  Magn Reson Chem, 45, 133-141.  
17601995 C.Yanofsky (2007).
RNA-based regulation of genes of tryptophan synthesis and degradation, in bacteria.
  RNA, 13, 1141-1154.  
18041896 F.Franceschi (2007).
Back to the future: the ribosome as an antibiotic target.
  Future Microbiol, 2, 571-574.  
17285172 I.A.Inverarity, and A.N.Hulme (2007).
Marked small molecule libraries: a truncated approach to molecular probe design.
  Org Biomol Chem, 5, 636-643.  
17245450 J.L.Baxter-Roshek, A.N.Petrov, and J.D.Dinman (2007).
Optimization of ribosome structure and function by rRNA base modification.
  PLoS ONE, 2, e174.  
17499045 K.L.Leach, S.M.Swaney, J.R.Colca, W.G.McDonald, J.R.Blinn, L.M.Thomasco, R.C.Gadwood, D.Shinabarger, L.Xiong, and A.S.Mankin (2007).
The site of action of oxazolidinone antibiotics in living bacteria and in human mitochondria.
  Mol Cell, 26, 393-402.  
17293420 L.R.Cruz-Vera, A.New, C.Squires, and C.Yanofsky (2007).
Ribosomal features essential for tna operon induction: tryptophan binding at the peptidyl transferase center.
  J Bacteriol, 189, 3140-3146.  
17321546 S.J.Schroeder, G.Blaha, J.Tirado-Rives, T.A.Steitz, and P.B.Moore (2007).
The structures of antibiotics bound to the E site region of the 50 S ribosomal subunit of Haloarcula marismortui: 13-deoxytedanolide and girodazole.
  J Mol Biol, 367, 1471-1479.
PDB codes: 2otj 2otl
17664317 S.J.Schroeder, G.Blaha, and P.B.Moore (2007).
Negamycin binds to the wall of the nascent chain exit tunnel of the 50S ribosomal subunit.
  Antimicrob Agents Chemother, 51, 4462-4465.
PDB code: 2qex
17555436 S.M.Toh, L.Xiong, C.A.Arias, M.V.Villegas, K.Lolans, J.Quinn, and A.S.Mankin (2007).
Acquisition of a natural resistance gene renders a clinical strain of methicillin-resistant Staphylococcus aureus resistant to the synthetic antibiotic linezolid.
  Mol Microbiol, 64, 1506-1514.  
17956547 S.Zaman, M.Fitzpatrick, L.Lindahl, and J.Zengel (2007).
Novel mutations in ribosomal proteins L4 and L22 that confer erythromycin resistance in Escherichia coli.
  Mol Microbiol, 66, 1039-1050.  
17959604 T.Kumasaka, M.Yamamoto, M.Furuichi, M.Nakasako, A.H.Teh, M.Kimura, I.Yamaguchi, and T.Ueki (2007).
Crystal Structures of Blasticidin S Deaminase (BSD): IMPLICATIONS FOR DYNAMIC PROPERTIES OF CATALYTIC ZINC.
  J Biol Chem, 282, 37103-37111.
PDB codes: 1wn5 1wn6 2z3g 2z3h 2z3i 2z3j
16773394 G.Papadopoulos, S.Grudinin, D.L.Kalpaxis, and T.Choli-Papadopoulou (2006).
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis.
  Eur Biophys J, 35, 675-683.  
17160060 J.Clardy, M.A.Fischbach, and C.T.Walsh (2006).
New antibiotics from bacterial natural products.
  Nat Biotechnol, 24, 1541-1550.  
16724458 J.Donarski, C.Shammas, R.Banks, and V.Ramesh (2006).
NMR and molecular modelling studies of the binding of amicetin antibiotic to conserved secondary structural motifs of 23S ribosomal RNAs.
  J Antibiot (Tokyo), 59, 177-183.  
16607023 K.L.Muldoon-Jacobs, and J.D.Dinman (2006).
Specific effects of ribosome-tethered molecular chaperones on programmed -1 ribosomal frameshifting.
  Eukaryot Cell, 5, 762-770.  
16642528 L.L.Grochowski, and T.M.Zabriskie (2006).
Characterization of BlsM, a nucleotide hydrolase involved in cytosine production for the biosynthesis of blasticidin S.
  Chembiochem, 7, 957-964.  
17055412 N.Foloppe, N.Matassova, and F.Aboul-Ela (2006).
Towards the discovery of drug-like RNA ligands?
  Drug Discov Today, 11, 1019-1027.  
16788184 P.B.Lodato, E.J.Rogers, and P.S.Lovett (2006).
A variation of the translation attenuation model can explain the inducible regulation of the pBC16 tetracycline resistance gene in Bacillus subtilis.
  J Bacteriol, 188, 4749-4758.  
17000775 R.Rakauskaite, and J.D.Dinman (2006).
An arc of unpaired "hinge bases" facilitates information exchange among functional centers of the ribosome.
  Mol Cell Biol, 26, 8992-9002.  
16888324 S.Mansouri, E.Nourollahzadeh, and K.A.Hudak (2006).
Pokeweed antiviral protein depurinates the sarcin/ricin loop of the rRNA prior to binding of aminoacyl-tRNA to the ribosomal A-site.
  RNA, 12, 1683-1692.  
16702403 T.C.Fleischer, C.M.Weaver, K.J.McAfee, J.L.Jennings, and A.J.Link (2006).
Systematic identification and functional screens of uncharacterized proteins associated with eukaryotic ribosomal complexes.
  Genes Dev, 20, 1294-1307.  
16553874 T.Tenson, and A.Mankin (2006).
Antibiotics and the ribosome.
  Mol Microbiol, 59, 1664-1677.  
17031058 Y.Kobayashi, M.Mizunuma, H.Osada, and T.Miyakawa (2006).
Identification of Saccharomyces cerevisiae ribosomal protein L3 as a target of curvularol, a G1-specific inhibitor of mammalian cells.
  Biosci Biotechnol Biochem, 70, 2451-2459.  
16314511 A.Meskauskas, A.N.Petrov, and J.D.Dinman (2005).
Identification of functionally important amino acids of ribosomal protein L3 by saturation mutagenesis.
  Mol Cell Biol, 25, 10863-10874.  
16244130 A.Tsagkalia, F.Leontiadou, M.A.Xaplanteri, G.Papadopoulos, D.L.Kalpaxis, and T.Choli-Papadopoulou (2005).
Ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus display multiple defects in ribosomal functions and sensitivity against erythromycin.
  RNA, 11, 1633-1639.  
16180279 A.Yonath (2005).
Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation.
  Annu Rev Biochem, 74, 649-679.  
15616575 D.N.Wilson, F.Schluenzen, J.M.Harms, T.Yoshida, T.Ohkubo, R.Albrecht, J.Buerger, Y.Kobayashi, and P.Fucini (2005).
X-ray crystallography study on ribosome recycling: the mechanism of binding and action of RRF on the 50S ribosomal subunit.
  EMBO J, 24, 251-260.
PDB code: 1y69
16336118 D.N.Wilson, J.M.Harms, K.H.Nierhaus, F.Schlünzen, and P.Fucini (2005).
Species-specific antibiotic-ribosome interactions: implications for drug development.
  Biol Chem, 386, 1239-1252.  
15851032 D.Tu, G.Blaha, P.B.Moore, and T.A.Steitz (2005).
Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance.
  Cell, 121, 257-270.
PDB codes: 1yhq 1yi2 1yij 1yit 1yj9 1yjn 1yjw
16127068 E.E.Nagiec, L.Wu, S.M.Swaney, J.G.Chosay, D.E.Ross, J.K.Brieland, and K.L.Leach (2005).
Oxazolidinones inhibit cellular proliferation via inhibition of mitochondrial protein synthesis.
  Antimicrob Agents Chemother, 49, 3896-3902.  
16111914 J.A.Sutcliffe (2005).
Improving on nature: antibiotics that target the ribosome.
  Curr Opin Microbiol, 8, 534-542.  
15834559 J.Dang, R.P.Metzger, R.T.Brownlee, C.A.Ng, M.Bergdahl, and F.Separovic (2005).
The conformational flexibility of the antibiotic virginiamycin M(1).
  Eur Biophys J, 34, 383-388.  
15980485 J.Kleinjung, and F.Fraternali (2005).
POPSCOMP: an automated interaction analysis of biomolecular complexes.
  Nucleic Acids Res, 33, W342-W346.  
16261170 J.Poehlsgaard, and S.Douthwaite (2005).
The bacterial ribosome as a target for antibiotics.
  Nat Rev Microbiol, 3, 870-881.  
15958059 K.H.Lee, S.Nishimura, S.Matsunaga, N.Fusetani, S.Horinouchi, and M.Yoshida (2005).
Inhibition of protein synthesis and activation of stress-activated protein kinases by onnamide A and theopederin B, antitumor marine natural products.
  Cancer Sci, 96, 357-364.  
15616280 M.Tanaka, T.Hasegawa, A.Okamoto, K.Torii, and M.Ohta (2005).
Effect of antibiotics on group A Streptococcus exoprotein production analyzed by two-dimensional gel electrophoresis.
  Antimicrob Agents Chemother, 49, 88-96.  
16257828 N.Polacek, and A.S.Mankin (2005).
The ribosomal peptidyl transferase center: structure, function, evolution, inhibition.
  Crit Rev Biochem Mol Biol, 40, 285-311.  
15950868 P.B.Moore, and T.A.Steitz (2005).
The ribosome revealed.
  Trends Biochem Sci, 30, 281-283.  
15995195 S.T.Gregory, J.F.Carr, D.Rodriguez-Correa, and A.E.Dahlberg (2005).
Mutational analysis of 16S and 23S rRNA genes of Thermus thermophilus.
  J Bacteriol, 187, 4804-4812.  
16244128 T.Dale, and O.C.Uhlenbeck (2005).
Binding of misacylated tRNAs to the ribosomal A site.
  RNA, 11, 1610-1615.  
15919197 T.Hermann (2005).
Drugs targeting the ribosome.
  Curr Opin Struct Biol, 15, 355-366.  
15075341 A.D.Petropoulos, M.A.Xaplanteri, G.P.Dinos, D.N.Wilson, and D.L.Kalpaxis (2004).
Polyamines affect diversely the antibiotic potency: insight gained from kinetic studies of the blasticidin S AND spiramycin interactions with functional ribosomes.
  J Biol Chem, 279, 26518-26525.  
15487937 A.Yonath, and A.Bashan (2004).
Ribosomal crystallography: initiation, peptide bond formation, and amino acid polymerization are hampered by antibiotics.
  Annu Rev Microbiol, 58, 233-251.  
15593140 B.François, J.Szychowski, S.S.Adhikari, K.Pachamuthu, E.E.Swayze, R.H.Griffey, M.T.Migawa, E.Westhof, and S.Hanessian (2004).
Antibacterial aminoglycosides with a modified mode of binding to the ribosomal-RNA decoding site.
  Angew Chem Int Ed Engl, 43, 6735-6738.
PDB codes: 2be0 2bee
15331605 D.Pettigrew, K.L.Anderson, J.Billington, E.Cota, P.Simpson, P.Urvil, F.Rabuzin, P.Roversi, B.Nowicki, L.du Merle, C.Le Bouguénec, S.Matthews, and S.M.Lea (2004).
High resolution studies of the Afa/Dr adhesin DraE and its interaction with chloramphenicol.
  J Biol Chem, 279, 46851-46857.
PDB codes: 1usq 1usz 1ut1 1ut2
15554968 F.Schlünzen, E.Pyetan, P.Fucini, A.Yonath, and J.M.Harms (2004).
Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin.
  Mol Microbiol, 54, 1287-1294.
PDB code: 1xbp
15066119 H.Yoshida, H.Yamamoto, T.Uchiumi, and A.Wada (2004).
RMF inactivates ribosomes by covering the peptidyl transferase centre and entrance of peptide exit tunnel.
  Genes Cells, 9, 271-278.  
15561995 J.L.Jacobs, and J.D.Dinman (2004).
Systematic analysis of bicistronic reporter assay data.
  Nucleic Acids Res, 32, e160.  
15059283 J.M.Harms, F.Schlünzen, P.Fucini, H.Bartels, and A.Yonath (2004).
Alterations at the peptidyl transferase centre of the ribosome induced by the synergistic action of the streptogramins dalfopristin and quinupristin.
  BMC Biol, 2, 4.
PDB code: 1sm1
15561874 J.Thompson, C.A.Pratt, and A.E.Dahlberg (2004).
Effects of a number of classes of 50S inhibitors on stop codon readthrough during protein synthesis.
  Antimicrob Agents Chemother, 48, 4889-4891.  
15509870 M.O'Connor, S.T.Gregory, and A.E.Dahlberg (2004).
Multiple defects in translation associated with altered ribosomal protein L4.
  Nucleic Acids Res, 32, 5750-5756.  
15554969 M.Pringle, J.Poehlsgaard, B.Vester, and K.S.Long (2004).
Mutations in ribosomal protein L3 and 23S ribosomal RNA at the peptidyl transferase centre are associated with reduced susceptibility to tiamulin in Brachyspira spp. isolates.
  Mol Microbiol, 54, 1295-1306.  
  15155144 N.Georgopapadakou (2004).
Superbugs and Superdrugs: a focus on antibacterials--6th annual SMi conference.
  Expert Opin Emerg Drugs, 9, 191-195.  
15016354 P.Auffinger, L.Bielecki, and E.Westhof (2004).
Anion binding to nucleic acids.
  Structure, 12, 379-388.  
15602549 R.R.Breaker (2004).
Natural and engineered nucleic acids as tools to explore biology.
  Nature, 432, 838-845.  
15491801 T.Auerbach, A.Bashan, and A.Yonath (2004).
Ribosomal antibiotics: structural basis for resistance, synergism and selectivity.
  Trends Biotechnol, 22, 570-576.  
15469510 V.Vimberg, L.Xiong, M.Bailey, T.Tenson, and A.Mankin (2004).
Peptide-mediated macrolide resistance reveals possible specific interactions in the nascent peptide exit tunnel.
  Mol Microbiol, 54, 376-385.  
14654696 K.S.Long, and B.T.Porse (2003).
A conserved chloramphenicol binding site at the entrance to the ribosomal peptide exit tunnel.
  Nucleic Acids Res, 31, 7208-7215.  
14523919 Q.Vicens, and E.Westhof (2003).
RNA as a drug target: the case of aminoglycosides.
  Chembiochem, 4, 1018-1023.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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