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PDBsum entry 1k8a
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protein dna_rna ligands metals Protein-protein interface(s) links
Ribosome PDB id
1k8a

 

 

 

 

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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
CAI
Metals
__K ×3
_NA ×83
_CL ×23
_MG ×119
_CD ×5
Waters ×7850
* Residue conservation analysis
PDB id:
1k8a
Name: Ribosome
Title: Co-crystal structure of carbomycin a bound to the 50s ribosomal subunit of haloarcula marismortui
Structure: 23s rrna. Chain: a. 5s rrna. Chain: b. Ribosomal protein l2. Chain: c. Synonym: 50s ribosomal protein l2p, hmal2, hl4. Ribosomal protein l3. Chain: d.
Source: Haloarcula marismortui. Organism_taxid: 2238. Organism_taxid: 2238
Resolution:
3.00Å     R-factor:   0.227     R-free:   0.265
Authors: J.L.Hansen,J.A.Ippolito,N.Ban,P.Nissen,P.B.Moore,T.Steitz
Key ref:
J.L.Hansen et al. (2002). The structures of four macrolide antibiotics bound to the large ribosomal subunit. Mol Cell, 10, 117-128. PubMed id: 12150912 DOI: 10.1016/S1097-2765(02)00570-1
Date:
23-Oct-01     Release date:   19-Jul-02    
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/S1097-2765(02)00570-1 Mol Cell 10:117-128 (2002)
PubMed id: 12150912  
 
 
The structures of four macrolide antibiotics bound to the large ribosomal subunit.
J.L.Hansen, J.A.Ippolito, N.Ban, P.Nissen, P.B.Moore, T.A.Steitz.
 
  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.
 
  Selected figure(s)  
 
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.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.
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20375101 A.Chirkova, M.D.Erlacher, N.Clementi, M.Zywicki, M.Aigner, and N.Polacek (2010).
The role of the universally conserved A2450-C2063 base pair in the ribosomal peptidyl transferase center.
  Nucleic Acids Res, 38, 4844-4855.  
20534348 A.L.Starosta, V.V.Karpenko, A.V.Shishkina, A.Mikolajka, N.V.Sumbatyan, F.Schluenzen, G.A.Korshunova, A.A.Bogdanov, and D.N.Wilson (2010).
Interplay between the ribosomal tunnel, nascent chain, and macrolides influences drug inhibition.
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20090988 B.Yang, T.Zöllner, P.Gebhardt, U.Möllmann, and M.J.Miller (2010).
Preparation and biological evaluation of novel leucomycin analogs derived from nitroso Diels-Alder reactions.
  Org Biomol Chem, 8, 691-697.  
20852642 C.L.Ng, K.Lang, N.A.Meenan, A.Sharma, A.C.Kelley, C.Kleanthous, and V.Ramakrishnan (2010).
Structural basis for 16S ribosomal RNA cleavage by the cytotoxic domain of colicin E3.
  Nat Struct Mol Biol, 17, 1241-1246.
PDB codes: 2xfz 2xg0 2xg1 2xg2
20876130 D.Bulkley, C.A.Innis, G.Blaha, and T.A.Steitz (2010).
Revisiting the structures of several antibiotics bound to the bacterial ribosome.
  Proc Natl Acad Sci U S A, 107, 17158-17163.
PDB codes: 3oge 3ogy 3oh5 3oh7 3ohc 3ohd 3ohj 3ohk 3ohy 3ohz 3oi0 3oi1 3oi2 3oi3 3oi4 3oi5
20446033 E.Cundliffe, and A.L.Demain (2010).
Avoidance of suicide in antibiotic-producing microbes.
  J Ind Microbiol Biotechnol, 37, 643-672.  
20439613 H.C.Nguyen, F.Karray, S.Lautru, J.Gagnat, A.Lebrihi, T.D.Huynh, and J.L.Pernodet (2010).
Glycosylation steps during spiramycin biosynthesis in Streptomyces ambofaciens: involvement of three glycosyltransferases and their interplay with two auxiliary proteins.
  Antimicrob Agents Chemother, 54, 2830-2839.  
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
20955199 L.Bidou, J.P.Rousset, and O.Namy (2010).
Translational errors: from yeast to new therapeutic targets.
  FEMS Yeast Res, 10, 1070-1082.  
20876111 S.Douthwaite (2010).
Designer drugs for discerning bugs.
  Proc Natl Acad Sci U S A, 107, 17065-17066.  
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
19929179 D.N.Wilson (2009).
The A-Z of bacterial translation inhibitors.
  Crit Rev Biochem Mol Biol, 44, 393-433.  
19164155 E.C.Kouvela, D.L.Kalpaxis, D.N.Wilson, and G.P.Dinos (2009).
Distinct mode of interaction of a novel ketolide antibiotic that displays enhanced antimicrobial activity.
  Antimicrob Agents Chemother, 53, 1411-1419.  
19150357 E.J.Diner, and C.S.Hayes (2009).
Recombineering reveals a diverse collection of ribosomal proteins L4 and L22 that confer resistance to macrolide antibiotics.
  J Mol Biol, 386, 300-315.  
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.  
19178182 J.B.Thoden, C.Schäffer, P.Messner, and H.M.Holden (2009).
Structural analysis of QdtB, an aminotransferase required for the biosynthesis of dTDP-3-acetamido-3,6-dideoxy-alpha-D-glucose.
  Biochemistry, 48, 1553-1561.
PDB code: 3frk
19124459 S.Li, H.Ouellet, D.H.Sherman, and L.M.Podust (2009).
Analysis of Transient and Catalytic Desosamine-binding Pockets in Cytochrome P-450 PikC from Streptomyces venezuelae.
  J Biol Chem, 284, 5723-5730.
PDB codes: 2vsj 2vz7 2vzm
20025795 X.Agirrezabala, and J.Frank (2009).
Elongation in translation as a dynamic interaction among the ribosome, tRNA, and elongation factors EF-G and EF-Tu.
  Q Rev Biophys, 42, 159-200.  
18079110 A.D.Petropoulos, E.C.Kouvela, G.P.Dinos, and D.L.Kalpaxis (2008).
Stepwise binding of tylosin and erythromycin to Escherichia coli ribosomes, characterized by kinetic and footprinting analysis.
  J Biol Chem, 283, 4756-4765.  
18218702 A.S.Bommakanti, L.Lindahl, and J.M.Zengel (2008).
Mutation from guanine to adenine in 25S rRNA at the position equivalent to E. coli A2058 does not confer erythromycin sensitivity in Sacchromyces cerevisae.
  RNA, 14, 460-464.  
18804176 A.S.Mankin (2008).
Macrolide myths.
  Curr Opin Microbiol, 11, 414-421.  
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.  
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.
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18510306 C.Guilbert, and T.L.James (2008).
Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets.
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18282091 D.L.Theobald, and D.S.Wuttke (2008).
Accurate structural correlations from maximum likelihood superpositions.
  PLoS Comput Biol, 4, e43.  
18406324 J.M.Harms, D.N.Wilson, F.Schluenzen, S.R.Connell, T.Stachelhaus, Z.Zaborowska, C.M.Spahn, and P.Fucini (2008).
Translational regulation via L11: molecular switches on the ribosome turned on and off by thiostrepton and micrococcin.
  Mol Cell, 30, 26-38.
PDB codes: 2zjp 2zjq 2zjr 3cf5
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.  
18084270 M.S.Jurica (2008).
Searching for a wrench to throw into the splicing machine.
  Nat Chem Biol, 4, 3-6.  
18160411 N.J.Reiter, L.J.Maher, and S.E.Butcher (2008).
DNA mimicry by a high-affinity anti-NF-kappaB RNA aptamer.
  Nucleic Acids Res, 36, 1227-1236.
PDB code: 2jwv
18439898 N.Vazquez-Laslop, C.Thum, and A.S.Mankin (2008).
Molecular mechanism of drug-dependent ribosome stalling.
  Mol Cell, 30, 190-202.  
18820754 R.E.Taylor (2008).
Tedanolide and the evolution of polyketide inhibitors of eukaryotic protein synthesis.
  Nat Prod Rep, 25, 854-861.  
18025251 S.M.Toh, L.Xiong, T.Bae, and A.S.Mankin (2008).
The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA.
  RNA, 14, 98.  
18382121 T.A.Steitz (2008).
Structural insights into the functions of the large ribosomal subunit, a major antibiotic target.
  Keio J Med, 57, 1.  
17110371 A.B.Sidhu, Q.Sun, L.J.Nkrumah, M.W.Dunne, J.C.Sacchettini, and D.A.Fidock (2007).
In vitro efficacy, resistance selection, and structural modeling studies implicate the malarial parasite apicoplast as the target of azithromycin.
  J Biol Chem, 282, 2494-2504.  
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.  
17630700 E.S.Burgie, and H.M.Holden (2007).
Molecular architecture of DesI: a key enzyme in the biosynthesis of desosamine.
  Biochemistry, 46, 8999-9006.
PDB code: 2po3
18041896 F.Franceschi (2007).
Back to the future: the ribosome as an antibiotic target.
  Future Microbiol, 2, 571-574.  
17048124 F.Leontiadou, A.Tsagkalia, and T.Choli-Papadopoulou (2007).
Thermus thermophilus L4 ribosomal protein: purification and sensitivity alteration against erythromycin of E. coli cells harboring a single amino acid mutant of TthL4 within its extended loop.
  Amino Acids, 33, 463-468.  
17476984 G.A.Korshunova, N.V.Sumbatian, N.V.Fedorova, I.V.Kuznetsova, A.V.Shishkina, and A.A.Bogdanov (2007).
[Peptide derivatives of tylosin-related macrolides]
  Bioorg Khim, 33, 235-244.  
17169991 H.R.Jonker, S.Ilin, S.K.Grimm, J.Wöhnert, and H.Schwalbe (2007).
L11 domain rearrangement upon binding to RNA and thiostrepton studied by NMR spectroscopy.
  Nucleic Acids Res, 35, 441-454.
PDB codes: 2jq7 2nyo
17159922 L.L.Silver (2007).
Multi-targeting by monotherapeutic antibacterials.
  Nat Rev Drug Discov, 6, 41-55.  
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
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.  
16962654 A.Korostelev, S.Trakhanov, M.Laurberg, and H.F.Noller (2006).
Crystal structure of a 70S ribosome-tRNA complex reveals functional interactions and rearrangements.
  Cell, 126, 1065-1077.
PDB codes: 1vsa 2ow8
17129165 C.Hyeon, R.I.Dima, and D.Thirumalai (2006).
Size, shape, and flexibility of RNA structures.
  J Chem Phys, 125, 194905.  
17441081 D.A.Thayer, and C.H.Wong (2006).
Vancomycin analogues containing monosaccharides exhibit improved antibiotic activity: a combined one-pot enzymatic glycosylation and chemical diversification strategy.
  Chem Asian J, 1, 445-452.  
16825192 D.H.Sherman, S.Li, L.V.Yermalitskaya, Y.Kim, J.A.Smith, M.R.Waterman, and L.M.Podust (2006).
The structural basis for substrate anchoring, active site selectivity, and product formation by P450 PikC from Streptomyces venezuelae.
  J Biol Chem, 281, 26289-26297.
PDB codes: 2bvj 2c6h 2c7x 2cd8
16490268 E.C.Böttger (2006).
The ribosome as a drug target.
  Trends Biotechnol, 24, 145-147.  
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.  
16717405 H.Yoneyama, and R.Katsumata (2006).
Antibiotic resistance in bacteria and its future for novel antibiotic development.
  Biosci Biotechnol Biochem, 70, 1060-1075.  
17160060 J.Clardy, M.A.Fischbach, and C.T.Walsh (2006).
New antibiotics from bacterial natural products.
  Nat Biotechnol, 24, 1541-1550.  
16410246 M.Lovmar, K.Nilsson, V.Vimberg, T.Tenson, M.Nervall, and M.Ehrenberg (2006).
The molecular mechanism of peptide-mediated erythromycin resistance.
  J Biol Chem, 281, 6742-6750.  
17032763 N.S.Sato, N.Hirabayashi, I.Agmon, A.Yonath, and T.Suzuki (2006).
Comprehensive genetic selection revealed essential bases in the peptidyl-transferase center.
  Proc Natl Acad Sci U S A, 103, 15386-15391.  
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.  
16923950 R.Berisio, N.Corti, P.Pfister, A.Yonath, and E.C.Böttger (2006).
23S rRNA 2058A-->G alteration mediates ketolide resistance in combination with deletion in L22.
  Antimicrob Agents Chemother, 50, 3816-3823.  
16538696 S.A.Borisova, C.Zhang, H.Takahashi, H.Zhang, A.W.Wong, J.S.Thorson, and H.W.Liu (2006).
Substrate specificity of the macrolide-glycosylating enzyme pair DesVII/DesVIII: opportunities, limitations, and mechanistic hypotheses.
  Angew Chem Int Ed Engl, 45, 2748-2753.  
16553874 T.Tenson, and A.Mankin (2006).
Antibiotics and the ribosome.
  Mol Microbiol, 59, 1664-1677.  
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.  
15936901 C.M.Wu, H.Wu, Y.Ning, J.Wang, X.Du, and J.Shen (2005).
Induction of macrolide resistance in Mycoplasma gallisepticum in vitro and its resistance-related mutations within domain V of 23S rRNA.
  FEMS Microbiol Lett, 247, 199-205.  
16174779 C.T.Madsen, L.Jakobsen, K.Buriánková, F.Doucet-Populaire, J.L.Pernodet, and S.Douthwaite (2005).
Methyltransferase Erm(37) slips on rRNA to confer atypical resistance in Mycobacterium tuberculosis.
  J Biol Chem, 280, 38942-38947.  
15853795 D.E.Brodersen, and P.Nissen (2005).
The social life of ribosomal proteins.
  FEBS J, 272, 2098-2108.  
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.  
15970993 D.Tu, G.Blaha, P.B.Moore, and T.A.Steitz (2005).
Gene replacement in Haloarcula marismortui: construction of a strain with two of its three chromosomal rRNA operons deleted.
  Extremophiles, 9, 427-435.  
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
16141058 H.F.Noller (2005).
RNA structure: reading the ribosome.
  Science, 309, 1508-1514.  
16096836 J.A.Silvers, and W.S.Champney (2005).
Accumulation and turnover of 23S ribosomal RNA in azithromycin-inhibited ribonuclease mutant strains of Escherichia coli.
  Arch Microbiol, 184, 66-77.  
16111914 J.A.Sutcliffe (2005).
Improving on nature: antibiotics that target the ribosome.
  Curr Opin Microbiol, 8, 534-542.  
15980485 J.Kleinjung, and F.Fraternali (2005).
POPSCOMP: an automated interaction analysis of biomolecular complexes.
  Nucleic Acids Res, 33, W342-W346.  
15793137 J.Poehlsgaard, P.Pfister, E.C.Böttger, and S.Douthwaite (2005).
Molecular mechanisms by which rRNA mutations confer resistance to clindamycin.
  Antimicrob Agents Chemother, 49, 1553-1555.  
16261170 J.Poehlsgaard, and S.Douthwaite (2005).
The bacterial ribosome as a target for antibiotics.
  Nat Rev Microbiol, 3, 870-881.  
16048949 K.Yan, E.Hunt, J.Berge, E.May, R.A.Copeland, and R.R.Gontarek (2005).
Fluorescence polarization method to characterize macrolide-ribosome interactions.
  Antimicrob Agents Chemother, 49, 3367-3372.  
15616307 L.Xiong, Y.Korkhin, and A.S.Mankin (2005).
Binding site of the bridged macrolides in the Escherichia coli ribosome.
  Antimicrob Agents Chemother, 49, 281-288.  
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.  
15795375 P.Pfister, N.Corti, S.Hobbie, C.Bruell, R.Zarivach, A.Yonath, and E.C.Böttger (2005).
23S rRNA base pair 2057-2611 determines ketolide susceptibility and fitness cost of the macrolide resistance mutation 2058A-->G.
  Proc Natl Acad Sci U S A, 102, 5180-5185.  
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.  
15919197 T.Hermann (2005).
Drugs targeting the ribosome.
  Curr Opin Struct Biol, 15, 355-366.  
16201934 T.Stakenborg, J.Vicca, P.Butaye, D.Maes, F.C.Minion, J.Peeters, A.De Kruif, and F.Haesebrouck (2005).
Characterization of In Vivo acquired resistance of Mycoplasma hyopneumoniae to macrolides and lincosamides.
  Microb Drug Resist, 11, 290-294.  
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.  
14760746 A.Lindner, and F.Hollfelder (2004).
European Symposium of Bio-Organic Chemistry 2003 (ESBOC): the evolution of catalysis.
  Chembiochem, 5, 241-243.  
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
15006354 C.A.Woolhead, P.J.McCormick, and A.E.Johnson (2004).
Nascent membrane and secretory proteins differ in FRET-detected folding far inside the ribosome and in their exposure to ribosomal proteins.
  Cell, 116, 725-736.  
15489173 C.D.Reeves, S.L.Ward, W.P.Revill, H.Suzuki, M.Marcus, O.V.Petrakovsky, S.Marquez, H.Fu, S.D.Dong, and L.Katz (2004).
Production of hybrid 16-membered macrolides by expressing combinations of polyketide synthase genes in engineered Streptomyces fradiae hosts.
  Chem Biol, 11, 1465-1472.  
15031493 C.T.Walsh (2004).
Polyketide and nonribosomal peptide antibiotics: modularity and versatility.
  Science, 303, 1805-1810.  
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
15554972 G.Stratigopoulos, N.Bate, and E.Cundliffe (2004).
Positive control of tylosin biosynthesis: pivotal role of TylR.
  Mol Microbiol, 54, 1326-1334.  
15388419 G.W.Novotny, L.Jakobsen, N.M.Andersen, J.Poehlsgaard, and S.Douthwaite (2004).
Ketolide antimicrobial activity persists after disruption of interactions with domain II of 23S rRNA.
  Antimicrob Agents Chemother, 48, 3677-3683.  
  15383170 H.B.Kim, B.Lee, H.C.Jang, S.H.Kim, C.I.Kang, Y.J.Choi, S.W.Park, B.S.Kim, E.C.Kim, M.D.Oh, and K.W.Choe (2004).
A high frequency of macrolide-lincosamide-streptogramin resistance determinants in Staphylococcus aureus isolated in South Korea.
  Microb Drug Resist, 10, 248-254.  
14695511 H.Nakatogawa, and K.Ito (2004).
Intraribosomal regulation of expression and fate of proteins.
  Chembiochem, 5, 48-51.  
15494397 J.Collier, C.Bohn, and P.Bouloc (2004).
SsrA tagging of Escherichia coli SecM at its translation arrest sequence.
  J Biol Chem, 279, 54193-54201.  
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.  
14693532 K.Buriánková, F.Doucet-Populaire, O.Dorson, A.Gondran, J.C.Ghnassia, J.Weiser, and J.L.Pernodet (2004).
Molecular basis of intrinsic macrolide resistance in the Mycobacterium tuberculosis complex.
  Antimicrob Agents Chemother, 48, 143-150.  
14999102 K.Das, T.Acton, Y.Chiang, L.Shih, E.Arnold, and G.T.Montelione (2004).
Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site.
  Proc Natl Acad Sci U S A, 101, 4041-4046.
PDB code: 1p91
15001709 L.Cochella, and R.Green (2004).
Isolation of antibiotic resistance mutations in the rRNA by using an in vitro selection system.
  Proc Natl Acad Sci U S A, 101, 3786-3791.  
15556400 M.Egli (2004).
Nucleic acid crystallography: current progress.
  Curr Opin Chem Biol, 8, 580-591.  
15388872 M.Liu, G.W.Novotny, and S.Douthwaite (2004).
Methylation of 23S rRNA nucleotide G745 is a secondary function of the RlmAI methyltransferase.
  RNA, 10, 1713-1720.  
15385552 M.Lovmar, T.Tenson, and M.Ehrenberg (2004).
Kinetics of macrolide action: the josamycin and erythromycin cases.
  J Biol Chem, 279, 53506-53515.  
14769948 O.Novac, A.S.Guenier, and J.Pelletier (2004).
Inhibitors of protein synthesis identified by a high throughput multiplexed translation screen.
  Nucleic Acids Res, 32, 902-915.  
15047540 O.Y.Misyurina, E.V.Chipitsyna, Y.P.Finashutina, V.N.Lazarev, T.A.Akopian, A.M.Savicheva, and V.M.Govorun (2004).
Mutations in a 23S rRNA gene of Chlamydia trachomatis associated with resistance to macrolides.
  Antimicrob Agents Chemother, 48, 1347-1349.  
15602549 R.R.Breaker (2004).
Natural and engineered nucleic acids as tools to explore biology.
  Nature, 432, 838-845.  
15561847 S.L.Ward, Z.Hu, A.Schirmer, R.Reid, W.P.Revill, C.D.Reeves, O.V.Petrakovsky, S.D.Dong, and L.Katz (2004).
Chalcomycin biosynthesis gene cluster from Streptomyces bikiniensis: novel features of an unusual ketolide produced through expression of the chm polyketide synthase in Streptomyces fradiae.
  Antimicrob Agents Chemother, 48, 4703-4712.  
14742195 S.Pereyre, C.Guyot, H.Renaudin, A.Charron, C.Bébéar, and C.M.Bébéar (2004).
In vitro selection and characterization of resistance to macrolides and related antibiotics in Mycoplasma pneumoniae.
  Antimicrob Agents Chemother, 48, 460-465.  
14570895 S.T.Allard, W.W.Cleland, and H.M.Holden (2004).
High resolution X-ray structure of dTDP-glucose 4,6-dehydratase from Streptomyces venezuelae.
  J Biol Chem, 279, 2211-2220.
PDB codes: 1r66 1r6d
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.  
15337844 Z.Druzina, and B.S.Cooperman (2004).
Photolabile anticodon stem-loop analogs of tRNAPhe as probes of ribosomal structure and structural fluctuation at the decoding center.
  RNA, 10, 1550-1562.  
12925991 A.Bashan, R.Zarivach, F.Schluenzen, I.Agmon, J.Harms, T.Auerbach, D.Baram, R.Berisio, H.Bartels, H.A.Hansen, P.Fucini, D.Wilson, M.Peretz, M.Kessler, and A.Yonath (2003).
Ribosomal crystallography: peptide bond formation and its inhibition.
  Biopolymers, 70, 19-41.  
  12930744 A.K.Bowers, J.A.Keller, and S.K.Dutcher (2003).
Molecular markers for rapidly identifying candidate genes in Chlamydomonas reinhardtii. Ery1 and ery2 encode chloroplast ribosomal proteins.
  Genetics, 164, 1345-1353.  
12583891 A.Vioque, and J.de la Cruz (2003).
Trans-translation and protein synthesis inhibitors.
  FEMS Microbiol Lett, 218, 9.  
14669983 A.Yonath (2003).
Ribosomal tolerance and peptide bond formation.
  Biol Chem, 384, 1411-1419.  
14523918 A.Yonath (2003).
Structural insight into functional aspects of ribosomal RNA targeting.
  Chembiochem, 4, 1008-1017.  
15040181 C.Walsh (2003).
Where will new antibiotics come from?
  Nat Rev Microbiol, 1, 65-70.  
12760848 D.J.Farrell, S.Douthwaite, I.Morrissey, S.Bakker, J.Poehlsgaard, L.Jakobsen, and D.Felmingham (2003).
Macrolide resistance by ribosomal mutation in clinical isolates of Streptococcus pneumoniae from the PROTEKT 1999-2000 study.
  Antimicrob Agents Chemother, 47, 1777-1783.  
12888505 D.R.Banatao, R.B.Altman, and T.E.Klein (2003).
Microenvironment analysis and identification of magnesium binding sites in RNA.
  Nucleic Acids Res, 31, 4450-4460.  
12623020 F.Schlünzen, J.M.Harms, F.Franceschi, H.A.Hansen, H.Bartels, R.Zarivach, and A.Yonath (2003).
Structural basis for the antibiotic activity of ketolides and azalides.
  Structure, 11, 329-338.
PDB codes: 1nwx 1nwy
14661991 G.G.Zhanel, T.Hisanaga, K.Nichol, A.Wierzbowski, and D.J.Hoban (2003).
Ketolides: an emerging treatment for macrolide-resistant respiratory infections, focusing on S. pneumoniae.
  Expert Opin Emerg Drugs, 8, 297-321.  
12907737 G.Maravić, J.M.Bujnicki, M.Feder, S.Pongor, and M.Flögel (2003).
Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC' redefines the substrate-binding site and suggests a model for protein-RNA interactions.
  Nucleic Acids Res, 31, 4941-4949.  
12787020 I.Agmon, T.Auerbach, D.Baram, H.Bartels, A.Bashan, R.Berisio, P.Fucini, H.A.Hansen, J.Harms, M.Kessler, M.Peretz, F.Schluenzen, A.Yonath, and R.Zarivach (2003).
On peptide bond formation, translocation, nascent protein progression and the regulatory properties of ribosomes. Derived on 20 October 2002 at the 28th FEBS Meeting in Istanbul.
  Eur J Biochem, 270, 2543-2556.  
12828631 I.Treede, L.Jakobsen, F.Kirpekar, B.Vester, G.Weitnauer, A.Bechthold, and S.Douthwaite (2003).
The avilamycin resistance determinants AviRa and AviRb methylate 23S rRNA at the guanosine 2535 base and the uridine 2479 ribose.
  Mol Microbiol, 49, 309-318.  
12499166 K.B.Waites, D.M.Crabb, and L.B.Duffy (2003).
In vitro activities of ABT-773 and other antimicrobials against human mycoplasmas.
  Antimicrob Agents Chemother, 47, 39-42.  
12750524 K.Fredrick, and H.F.Noller (2003).
Catalysis of ribosomal translocation by sparsomycin.
  Science, 300, 1159-1162.  
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.  
14709813 N.Prapasarakul, K.Ochi, and Y.Adachi (2003).
In vitro susceptibility and a new point mutation associated with tylosin-resistance in Japanese canine intestinal spirochetes.
  J Vet Med Sci, 65, 1275-1280.  
14527328 P.B.Moore, and T.A.Steitz (2003).
The structural basis of large ribosomal subunit function.
  Annu Rev Biochem, 72, 813-850.  
12709313 P.Pfister, M.Risch, D.E.Brodersen, and E.C.Böttger (2003).
Role of 16S rRNA Helix 44 in Ribosomal Resistance to Hygromycin B.
  Antimicrob Agents Chemother, 47, 1496-1502.  
14523919 Q.Vicens, and E.Westhof (2003).
RNA as a drug target: the case of aminoglycosides.
  Chembiochem, 4, 1018-1023.  
12665853 R.Berisio, F.Schluenzen, J.Harms, A.Bashan, T.Auerbach, D.Baram, and A.Yonath (2003).
Structural insight into the role of the ribosomal tunnel in cellular regulation.
  Nat Struct Biol, 10, 366-370.
PDB code: 1ond
12932729 T.A.Steitz, and P.B.Moore (2003).
RNA, the first macromolecular catalyst: the ribosome is a ribozyme.
  Trends Biochem Sci, 28, 411-418.  
12925990 T.Hermann (2003).
Chemical and functional diversity of small molecule ligands for RNA.
  Biopolymers, 70, 4.  
12821448 e.l.-.S.E.Habib, J.N.Scarsdale, and K.A.Reynolds (2003).
Biosynthetic origin of hygromycin A.
  Antimicrob Agents Chemother, 47, 2065-2071.  
12417742 M.Liu, and S.Douthwaite (2002).
Resistance to the macrolide antibiotic tylosin is conferred by single methylations at 23S rRNA nucleotides G748 and A2058 acting in synergy.
  Proc Natl Acad Sci U S A, 99, 14658-14663.  
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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